src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  63 import jalview.io.AlignmentProperties;
  64 import jalview.io.AnnotationFile;
  65 import jalview.io.BioJsHTMLOutput;
  66 import jalview.io.FileLoader;
  67 import jalview.io.FormatAdapter;
  68 import jalview.io.HtmlSvgOutput;
  69 import jalview.io.IdentifyFile;
  70 import jalview.io.JalviewFileChooser;
  71 import jalview.io.JalviewFileView;
  72 import jalview.io.JnetAnnotationMaker;
  73 import jalview.io.NewickFile;
  74 import jalview.io.StructureFile;
  75 import jalview.io.TCoffeeScoreFile;
  76 import jalview.jbgui.GAlignFrame;
  77 import jalview.schemes.Blosum62ColourScheme;
  78 import jalview.schemes.BuriedColourScheme;
  79 import jalview.schemes.ClustalxColourScheme;
  80 import jalview.schemes.ColourSchemeI;
  81 import jalview.schemes.ColourSchemeProperty;
  82 import jalview.schemes.HelixColourScheme;
  83 import jalview.schemes.HydrophobicColourScheme;
  84 import jalview.schemes.NucleotideColourScheme;
  85 import jalview.schemes.PIDColourScheme;
  86 import jalview.schemes.PurinePyrimidineColourScheme;
  87 import jalview.schemes.RNAHelicesColourChooser;
  88 import jalview.schemes.ResidueProperties;
  89 import jalview.schemes.StrandColourScheme;
  90 import jalview.schemes.TCoffeeColourScheme;
  91 import jalview.schemes.TaylorColourScheme;
  92 import jalview.schemes.TurnColourScheme;
  93 import jalview.schemes.UserColourScheme;
  94 import jalview.schemes.ZappoColourScheme;
  95 import jalview.util.MessageManager;
  96 import jalview.viewmodel.AlignmentViewport;
  97 import jalview.ws.DBRefFetcher;
  98 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  99 import jalview.ws.jws1.Discoverer;
 100 import jalview.ws.jws2.Jws2Discoverer;
 101 import jalview.ws.jws2.jabaws2.Jws2Instance;
 102 import jalview.ws.seqfetcher.DbSourceProxy;
 103
 104 import java.awt.BorderLayout;
 105 import java.awt.Component;
 106 import java.awt.Rectangle;
 107 import java.awt.Toolkit;
 108 import java.awt.datatransfer.Clipboard;
 109 import java.awt.datatransfer.DataFlavor;
 110 import java.awt.datatransfer.StringSelection;
 111 import java.awt.datatransfer.Transferable;
 112 import java.awt.dnd.DnDConstants;
 113 import java.awt.dnd.DropTargetDragEvent;
 114 import java.awt.dnd.DropTargetDropEvent;
 115 import java.awt.dnd.DropTargetEvent;
 116 import java.awt.dnd.DropTargetListener;
 117 import java.awt.event.ActionEvent;
 118 import java.awt.event.ActionListener;
 119 import java.awt.event.FocusAdapter;
 120 import java.awt.event.FocusEvent;
 121 import java.awt.event.ItemEvent;
 122 import java.awt.event.ItemListener;
 123 import java.awt.event.KeyAdapter;
 124 import java.awt.event.KeyEvent;
 125 import java.awt.event.MouseAdapter;
 126 import java.awt.event.MouseEvent;
 127 import java.awt.print.PageFormat;
 128 import java.awt.print.PrinterJob;
 129 import java.beans.PropertyChangeEvent;
 130 import java.io.File;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.JCheckBoxMenuItem;
 141 import javax.swing.JEditorPane;
 142 import javax.swing.JInternalFrame;
 143 import javax.swing.JLayeredPane;
 144 import javax.swing.JMenu;
 145 import javax.swing.JMenuItem;
 146 import javax.swing.JOptionPane;
 147 import javax.swing.JRadioButtonMenuItem;
 148 import javax.swing.JScrollPane;
 149 import javax.swing.SwingUtilities;
 150
 151 /**
 152  * DOCUMENT ME!
 153  *
 154  * @author $author$
 155  * @version $Revision$
 156  */
 157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 158         IProgressIndicator, AlignViewControllerGuiI
 159 {
 160
 161   public static final int DEFAULT_WIDTH = 700;
 162
 163   public static final int DEFAULT_HEIGHT = 500;
 164
 165   /*
 166    * The currently displayed panel (selected tabbed view if more than one)
 167    */
 168   public AlignmentPanel alignPanel;
 169
 170   AlignViewport viewport;
 171
 172   public AlignViewControllerI avc;
 173
 174   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 175
 176   /**
 177    * Last format used to load or save alignments in this window
 178    */
 179   String currentFileFormat = null;
 180
 181   /**
 182    * Current filename for this alignment
 183    */
 184   String fileName = null;
 185
 186   /**
 187    * Creates a new AlignFrame object with specific width and height.
 188    *
 189    * @param al
 190    * @param width
 191    * @param height
 192    */
 193   public AlignFrame(AlignmentI al, int width, int height)
 194   {
 195     this(al, null, width, height);
 196   }
 197
 198   /**
 199    * Creates a new AlignFrame object with specific width, height and
 200    * sequenceSetId
 201    *
 202    * @param al
 203    * @param width
 204    * @param height
 205    * @param sequenceSetId
 206    */
 207   public AlignFrame(AlignmentI al, int width, int height,
 208           String sequenceSetId)
 209   {
 210     this(al, null, width, height, sequenceSetId);
 211   }
 212
 213   /**
 214    * Creates a new AlignFrame object with specific width, height and
 215    * sequenceSetId
 216    *
 217    * @param al
 218    * @param width
 219    * @param height
 220    * @param sequenceSetId
 221    * @param viewId
 222    */
 223   public AlignFrame(AlignmentI al, int width, int height,
 224           String sequenceSetId, String viewId)
 225   {
 226     this(al, null, width, height, sequenceSetId, viewId);
 227   }
 228
 229   /**
 230    * new alignment window with hidden columns
 231    *
 232    * @param al
 233    *          AlignmentI
 234    * @param hiddenColumns
 235    *          ColumnSelection or null
 236    * @param width
 237    *          Width of alignment frame
 238    * @param height
 239    *          height of frame.
 240    */
 241   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 242           int width, int height)
 243   {
 244     this(al, hiddenColumns, width, height, null);
 245   }
 246
 247   /**
 248    * Create alignment frame for al with hiddenColumns, a specific width and
 249    * height, and specific sequenceId
 250    *
 251    * @param al
 252    * @param hiddenColumns
 253    * @param width
 254    * @param height
 255    * @param sequenceSetId
 256    *          (may be null)
 257    */
 258   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 259           int width, int height, String sequenceSetId)
 260   {
 261     this(al, hiddenColumns, width, height, sequenceSetId, null);
 262   }
 263
 264   /**
 265    * Create alignment frame for al with hiddenColumns, a specific width and
 266    * height, and specific sequenceId
 267    *
 268    * @param al
 269    * @param hiddenColumns
 270    * @param width
 271    * @param height
 272    * @param sequenceSetId
 273    *          (may be null)
 274    * @param viewId
 275    *          (may be null)
 276    */
 277   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 278           int width, int height, String sequenceSetId, String viewId)
 279   {
 280     setSize(width, height);
 281
 282     if (al.getDataset() == null)
 283     {
 284       al.setDataset(null);
 285     }
 286
 287     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 288
 289     alignPanel = new AlignmentPanel(this, viewport);
 290
 291     addAlignmentPanel(alignPanel, true);
 292     init();
 293   }
 294
 295   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 296           ColumnSelection hiddenColumns, int width, int height)
 297   {
 298     setSize(width, height);
 299
 300     if (al.getDataset() == null)
 301     {
 302       al.setDataset(null);
 303     }
 304
 305     viewport = new AlignViewport(al, hiddenColumns);
 306
 307     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 308     {
 309       viewport.hideSequence(hiddenSeqs);
 310     }
 311     alignPanel = new AlignmentPanel(this, viewport);
 312     addAlignmentPanel(alignPanel, true);
 313     init();
 314   }
 315
 316   /**
 317    * Make a new AlignFrame from existing alignmentPanels
 318    *
 319    * @param ap
 320    *          AlignmentPanel
 321    * @param av
 322    *          AlignViewport
 323    */
 324   public AlignFrame(AlignmentPanel ap)
 325   {
 326     viewport = ap.av;
 327     alignPanel = ap;
 328     addAlignmentPanel(ap, false);
 329     init();
 330   }
 331
 332   /**
 333    * initalise the alignframe from the underlying viewport data and the
 334    * configurations
 335    */
 336   void init()
 337   {
 338     if (!Jalview.isHeadlessMode())
 339     {
 340       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 341     }
 342
 343     avc = new jalview.controller.AlignViewController(this, viewport,
 344             alignPanel);
 345     if (viewport.getAlignmentConservationAnnotation() == null)
 346     {
 347       BLOSUM62Colour.setEnabled(false);
 348       conservationMenuItem.setEnabled(false);
 349       modifyConservation.setEnabled(false);
 350       // PIDColour.setEnabled(false);
 351       // abovePIDThreshold.setEnabled(false);
 352       // modifyPID.setEnabled(false);
 353     }
 354
 355     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 356             "No sort");
 357
 358     if (sortby.equals("Id"))
 359     {
 360       sortIDMenuItem_actionPerformed(null);
 361     }
 362     else if (sortby.equals("Pairwise Identity"))
 363     {
 364       sortPairwiseMenuItem_actionPerformed(null);
 365     }
 366
 367     if (Desktop.desktop != null)
 368     {
 369       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 370       addServiceListeners();
 371       setGUINucleotide(viewport.getAlignment().isNucleotide());
 372     }
 373
 374     this.alignPanel.av
 375             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 376
 377     setMenusFromViewport(viewport);
 378     buildSortByAnnotationScoresMenu();
 379     buildTreeMenu();
 380
 381     if (viewport.getWrapAlignment())
 382     {
 383       wrapMenuItem_actionPerformed(null);
 384     }
 385
 386     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 387     {
 388       this.overviewMenuItem_actionPerformed(null);
 389     }
 390
 391     addKeyListener();
 392
 393     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 394     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 395     final String menuLabel = MessageManager
 396             .getString("label.copy_format_from");
 397     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 398             new ViewSetProvider()
 399             {
 400
 401               @Override
 402               public AlignmentPanel[] getAllAlignmentPanels()
 403               {
 404                 origview.clear();
 405                 origview.add(alignPanel);
 406                 // make an array of all alignment panels except for this one
 407                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 408                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 409                 aps.remove(AlignFrame.this.alignPanel);
 410                 return aps.toArray(new AlignmentPanel[aps.size()]);
 411               }
 412             }, selviews, new ItemListener()
 413             {
 414
 415               @Override
 416               public void itemStateChanged(ItemEvent e)
 417               {
 418                 if (origview.size() > 0)
 419                 {
 420                   final AlignmentPanel ap = origview.get(0);
 421
 422                   /*
 423                    * Copy the ViewStyle of the selected panel to 'this one'.
 424                    * Don't change value of 'scaleProteinAsCdna' unless copying
 425                    * from a SplitFrame.
 426                    */
 427                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 428                           .getViewStyle();
 429                   boolean fromSplitFrame = selviews.get(0)
 430                           .getAlignViewport().getCodingComplement() != null;
 431                   if (!fromSplitFrame)
 432                   {
 433                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 434                             .getViewStyle().isScaleProteinAsCdna());
 435                   }
 436                   ap.getAlignViewport().setViewStyle(vs);
 437
 438                   /*
 439                    * Also rescale ViewStyle of SplitFrame complement if there is
 440                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 441                    * the whole ViewStyle (allow cDNA protein to have different
 442                    * fonts)
 443                    */
 444                   AlignViewportI complement = ap.getAlignViewport()
 445                           .getCodingComplement();
 446                   if (complement != null && vs.isScaleProteinAsCdna())
 447                   {
 448                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 449                     ((SplitFrame) af.getSplitViewContainer())
 450                             .adjustLayout();
 451                     af.setMenusForViewport();
 452                   }
 453
 454                   ap.updateLayout();
 455                   ap.setSelected(true);
 456                   ap.alignFrame.setMenusForViewport();
 457
 458                 }
 459               }
 460             });
 461     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 462             .indexOf("devel") > -1
 463             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 464                     .indexOf("test") > -1)
 465     {
 466       formatMenu.add(vsel);
 467     }
 468     addFocusListener(new FocusAdapter()
 469     {
 470       @Override
 471       public void focusGained(FocusEvent e)
 472       {
 473         Jalview.setCurrentAlignFrame(AlignFrame.this);
 474       }
 475     });
 476
 477   }
 478
 479   /**
 480    * Change the filename and format for the alignment, and enable the 'reload'
 481    * button functionality.
 482    *
 483    * @param file
 484    *          valid filename
 485    * @param format
 486    *          format of file
 487    */
 488   public void setFileName(String file, String format)
 489   {
 490     fileName = file;
 491     setFileFormat(format);
 492     reload.setEnabled(true);
 493   }
 494
 495   /**
 496    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 497    * events
 498    */
 499   void addKeyListener()
 500   {
 501     addKeyListener(new KeyAdapter()
 502     {
 503       @Override
 504       public void keyPressed(KeyEvent evt)
 505       {
 506         if (viewport.cursorMode
 507                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 508                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 509                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 510                 && Character.isDigit(evt.getKeyChar()))
 511         {
 512           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 513         }
 514
 515         switch (evt.getKeyCode())
 516         {
 517
 518         case 27: // escape key
 519           deselectAllSequenceMenuItem_actionPerformed(null);
 520
 521           break;
 522
 523         case KeyEvent.VK_DOWN:
 524           if (evt.isAltDown() || !viewport.cursorMode)
 525           {
 526             moveSelectedSequences(false);
 527           }
 528           if (viewport.cursorMode)
 529           {
 530             alignPanel.getSeqPanel().moveCursor(0, 1);
 531           }
 532           break;
 533
 534         case KeyEvent.VK_UP:
 535           if (evt.isAltDown() || !viewport.cursorMode)
 536           {
 537             moveSelectedSequences(true);
 538           }
 539           if (viewport.cursorMode)
 540           {
 541             alignPanel.getSeqPanel().moveCursor(0, -1);
 542           }
 543
 544           break;
 545
 546         case KeyEvent.VK_LEFT:
 547           if (evt.isAltDown() || !viewport.cursorMode)
 548           {
 549             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 550           }
 551           else
 552           {
 553             alignPanel.getSeqPanel().moveCursor(-1, 0);
 554           }
 555
 556           break;
 557
 558         case KeyEvent.VK_RIGHT:
 559           if (evt.isAltDown() || !viewport.cursorMode)
 560           {
 561             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 562           }
 563           else
 564           {
 565             alignPanel.getSeqPanel().moveCursor(1, 0);
 566           }
 567           break;
 568
 569         case KeyEvent.VK_SPACE:
 570           if (viewport.cursorMode)
 571           {
 572             alignPanel.getSeqPanel().insertGapAtCursor(
 573                     evt.isControlDown() || evt.isShiftDown()
 574                             || evt.isAltDown());
 575           }
 576           break;
 577
 578         // case KeyEvent.VK_A:
 579         // if (viewport.cursorMode)
 580         // {
 581         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 582         // //System.out.println("A");
 583         // }
 584         // break;
 585         /*
 586          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 587          * System.out.println("closing bracket"); } break;
 588          */
 589         case KeyEvent.VK_DELETE:
 590         case KeyEvent.VK_BACK_SPACE:
 591           if (!viewport.cursorMode)
 592           {
 593             cut_actionPerformed(null);
 594           }
 595           else
 596           {
 597             alignPanel.getSeqPanel().deleteGapAtCursor(
 598                     evt.isControlDown() || evt.isShiftDown()
 599                             || evt.isAltDown());
 600           }
 601
 602           break;
 603
 604         case KeyEvent.VK_S:
 605           if (viewport.cursorMode)
 606           {
 607             alignPanel.getSeqPanel().setCursorRow();
 608           }
 609           break;
 610         case KeyEvent.VK_C:
 611           if (viewport.cursorMode && !evt.isControlDown())
 612           {
 613             alignPanel.getSeqPanel().setCursorColumn();
 614           }
 615           break;
 616         case KeyEvent.VK_P:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorPosition();
 620           }
 621           break;
 622
 623         case KeyEvent.VK_ENTER:
 624         case KeyEvent.VK_COMMA:
 625           if (viewport.cursorMode)
 626           {
 627             alignPanel.getSeqPanel().setCursorRowAndColumn();
 628           }
 629           break;
 630
 631         case KeyEvent.VK_Q:
 632           if (viewport.cursorMode)
 633           {
 634             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 635           }
 636           break;
 637         case KeyEvent.VK_M:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 641           }
 642           break;
 643
 644         case KeyEvent.VK_F2:
 645           viewport.cursorMode = !viewport.cursorMode;
 646           statusBar.setText(MessageManager.formatMessage(
 647                   "label.keyboard_editing_mode",
 648                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 649           if (viewport.cursorMode)
 650           {
 651             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 652             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 653           }
 654           alignPanel.getSeqPanel().seqCanvas.repaint();
 655           break;
 656
 657         case KeyEvent.VK_F1:
 658           try
 659           {
 660             Help.showHelpWindow();
 661           } catch (Exception ex)
 662           {
 663             ex.printStackTrace();
 664           }
 665           break;
 666         case KeyEvent.VK_H:
 667         {
 668           boolean toggleSeqs = !evt.isControlDown();
 669           boolean toggleCols = !evt.isShiftDown();
 670           toggleHiddenRegions(toggleSeqs, toggleCols);
 671           break;
 672         }
 673         case KeyEvent.VK_PAGE_UP:
 674           if (viewport.getWrapAlignment())
 675           {
 676             alignPanel.scrollUp(true);
 677           }
 678           else
 679           {
 680             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 681                     - viewport.endSeq + viewport.startSeq);
 682           }
 683           break;
 684         case KeyEvent.VK_PAGE_DOWN:
 685           if (viewport.getWrapAlignment())
 686           {
 687             alignPanel.scrollUp(false);
 688           }
 689           else
 690           {
 691             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 692                     + viewport.endSeq - viewport.startSeq);
 693           }
 694           break;
 695         }
 696       }
 697
 698       @Override
 699       public void keyReleased(KeyEvent evt)
 700       {
 701         switch (evt.getKeyCode())
 702         {
 703         case KeyEvent.VK_LEFT:
 704           if (evt.isAltDown() || !viewport.cursorMode)
 705           {
 706             viewport.firePropertyChange("alignment", null, viewport
 707                     .getAlignment().getSequences());
 708           }
 709           break;
 710
 711         case KeyEvent.VK_RIGHT:
 712           if (evt.isAltDown() || !viewport.cursorMode)
 713           {
 714             viewport.firePropertyChange("alignment", null, viewport
 715                     .getAlignment().getSequences());
 716           }
 717           break;
 718         }
 719       }
 720     });
 721   }
 722
 723   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 724   {
 725     ap.alignFrame = this;
 726     avc = new jalview.controller.AlignViewController(this, viewport,
 727             alignPanel);
 728
 729     alignPanels.add(ap);
 730
 731     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 732
 733     int aSize = alignPanels.size();
 734
 735     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 736
 737     if (aSize == 1 && ap.av.viewName == null)
 738     {
 739       this.getContentPane().add(ap, BorderLayout.CENTER);
 740     }
 741     else
 742     {
 743       if (aSize == 2)
 744       {
 745         setInitialTabVisible();
 746       }
 747
 748       expandViews.setEnabled(true);
 749       gatherViews.setEnabled(true);
 750       tabbedPane.addTab(ap.av.viewName, ap);
 751
 752       ap.setVisible(false);
 753     }
 754
 755     if (newPanel)
 756     {
 757       if (ap.av.isPadGaps())
 758       {
 759         ap.av.getAlignment().padGaps();
 760       }
 761       ap.av.updateConservation(ap);
 762       ap.av.updateConsensus(ap);
 763       ap.av.updateStrucConsensus(ap);
 764     }
 765   }
 766
 767   public void setInitialTabVisible()
 768   {
 769     expandViews.setEnabled(true);
 770     gatherViews.setEnabled(true);
 771     tabbedPane.setVisible(true);
 772     AlignmentPanel first = alignPanels.get(0);
 773     tabbedPane.addTab(first.av.viewName, first);
 774     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 775   }
 776
 777   public AlignViewport getViewport()
 778   {
 779     return viewport;
 780   }
 781
 782   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 783   private void addServiceListeners()
 784   {
 785     final java.beans.PropertyChangeListener thisListener;
 786     Desktop.instance.addJalviewPropertyChangeListener("services",
 787             thisListener = new java.beans.PropertyChangeListener()
 788             {
 789               @Override
 790               public void propertyChange(PropertyChangeEvent evt)
 791               {
 792                 // // System.out.println("Discoverer property change.");
 793                 // if (evt.getPropertyName().equals("services"))
 794                 {
 795                   SwingUtilities.invokeLater(new Runnable()
 796                   {
 797
 798                     @Override
 799                     public void run()
 800                     {
 801                       System.err
 802                               .println("Rebuild WS Menu for service change");
 803                       BuildWebServiceMenu();
 804                     }
 805
 806                   });
 807                 }
 808               }
 809             });
 810     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 811     {
 812       @Override
 813       public void internalFrameClosed(
 814               javax.swing.event.InternalFrameEvent evt)
 815       {
 816         // System.out.println("deregistering discoverer listener");
 817         Desktop.instance.removeJalviewPropertyChangeListener("services",
 818                 thisListener);
 819         closeMenuItem_actionPerformed(true);
 820       };
 821     });
 822     // Finally, build the menu once to get current service state
 823     new Thread(new Runnable()
 824     {
 825       @Override
 826       public void run()
 827       {
 828         BuildWebServiceMenu();
 829       }
 830     }).start();
 831   }
 832
 833   /**
 834    * Configure menu items that vary according to whether the alignment is
 835    * nucleotide or protein
 836    *
 837    * @param nucleotide
 838    */
 839   public void setGUINucleotide(boolean nucleotide)
 840   {
 841     showTranslation.setVisible(nucleotide);
 842     showReverse.setVisible(nucleotide);
 843     showReverseComplement.setVisible(nucleotide);
 844     conservationMenuItem.setEnabled(!nucleotide);
 845     modifyConservation.setEnabled(!nucleotide);
 846     showGroupConservation.setEnabled(!nucleotide);
 847     rnahelicesColour.setEnabled(nucleotide);
 848     purinePyrimidineColour.setEnabled(nucleotide);
 849     showComplementMenuItem.setText(nucleotide ? MessageManager
 850             .getString("label.protein") : MessageManager
 851             .getString("label.nucleotide"));
 852     setColourSelected(jalview.bin.Cache.getDefault(
 853             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 854                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 855   }
 856
 857   /**
 858    * set up menus for the current viewport. This may be called after any
 859    * operation that affects the data in the current view (selection changed,
 860    * etc) to update the menus to reflect the new state.
 861    */
 862   @Override
 863   public void setMenusForViewport()
 864   {
 865     setMenusFromViewport(viewport);
 866   }
 867
 868   /**
 869    * Need to call this method when tabs are selected for multiple views, or when
 870    * loading from Jalview2XML.java
 871    *
 872    * @param av
 873    *          AlignViewport
 874    */
 875   void setMenusFromViewport(AlignViewport av)
 876   {
 877     padGapsMenuitem.setSelected(av.isPadGaps());
 878     colourTextMenuItem.setSelected(av.isShowColourText());
 879     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 880     conservationMenuItem.setSelected(av.getConservationSelected());
 881     seqLimits.setSelected(av.getShowJVSuffix());
 882     idRightAlign.setSelected(av.isRightAlignIds());
 883     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 884     renderGapsMenuItem.setSelected(av.isRenderGaps());
 885     wrapMenuItem.setSelected(av.getWrapAlignment());
 886     scaleAbove.setVisible(av.getWrapAlignment());
 887     scaleLeft.setVisible(av.getWrapAlignment());
 888     scaleRight.setVisible(av.getWrapAlignment());
 889     annotationPanelMenuItem.setState(av.isShowAnnotation());
 890     /*
 891      * Show/hide annotations only enabled if annotation panel is shown
 892      */
 893     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 894     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 895     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 898     viewTextMenuItem.setSelected(av.getShowText());
 899     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 900     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 901     showGroupConservation.setSelected(av.isShowGroupConservation());
 902     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 903     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 904     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 905
 906     setColourSelected(ColourSchemeProperty.getColourName(av
 907             .getGlobalColourScheme()));
 908
 909     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 910     hiddenMarkers.setState(av.getShowHiddenMarkers());
 911     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 912     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 913     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 914     autoCalculate.setSelected(av.autoCalculateConsensus);
 915     sortByTree.setSelected(av.sortByTree);
 916     listenToViewSelections.setSelected(av.followSelection);
 917     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 918     rnahelicesColour
 919             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 920
 921     showProducts.setEnabled(canShowProducts());
 922     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 923
 924     updateEditMenuBar();
 925   }
 926
 927   /**
 928    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 929    *
 930    * @param b
 931    */
 932   public void setGroovyEnabled(boolean b)
 933   {
 934     runGroovy.setEnabled(b);
 935   }
 936
 937   private IProgressIndicator progressBar;
 938
 939   /*
 940    * (non-Javadoc)
 941    *
 942    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 943    */
 944   @Override
 945   public void setProgressBar(String message, long id)
 946   {
 947     progressBar.setProgressBar(message, id);
 948   }
 949
 950   @Override
 951   public void registerHandler(final long id,
 952           final IProgressIndicatorHandler handler)
 953   {
 954     progressBar.registerHandler(id, handler);
 955   }
 956
 957   /**
 958    *
 959    * @return true if any progress bars are still active
 960    */
 961   @Override
 962   public boolean operationInProgress()
 963   {
 964     return progressBar.operationInProgress();
 965   }
 966
 967   @Override
 968   public void setStatus(String text)
 969   {
 970     statusBar.setText(text);
 971   }
 972
 973   /*
 974    * Added so Castor Mapping file can obtain Jalview Version
 975    */
 976   public String getVersion()
 977   {
 978     return jalview.bin.Cache.getProperty("VERSION");
 979   }
 980
 981   public FeatureRenderer getFeatureRenderer()
 982   {
 983     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 984   }
 985
 986   @Override
 987   public void fetchSequence_actionPerformed(ActionEvent e)
 988   {
 989     new jalview.gui.SequenceFetcher(this);
 990   }
 991
 992   @Override
 993   public void addFromFile_actionPerformed(ActionEvent e)
 994   {
 995     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 996   }
 997
 998   @Override
 999   public void reload_actionPerformed(ActionEvent e)
1000   {
1001     if (fileName != null)
1002     {
1003       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1004       // originating file's format
1005       // TODO: work out how to recover feature settings for correct view(s) when
1006       // file is reloaded.
1007       if (currentFileFormat.equals("Jalview"))
1008       {
1009         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1010         for (int i = 0; i < frames.length; i++)
1011         {
1012           if (frames[i] instanceof AlignFrame && frames[i] != this
1013                   && ((AlignFrame) frames[i]).fileName != null
1014                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1015           {
1016             try
1017             {
1018               frames[i].setSelected(true);
1019               Desktop.instance.closeAssociatedWindows();
1020             } catch (java.beans.PropertyVetoException ex)
1021             {
1022             }
1023           }
1024
1025         }
1026         Desktop.instance.closeAssociatedWindows();
1027
1028         FileLoader loader = new FileLoader();
1029         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1030         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1031       }
1032       else
1033       {
1034         Rectangle bounds = this.getBounds();
1035
1036         FileLoader loader = new FileLoader();
1037         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1038         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1039                 protocol, currentFileFormat);
1040
1041         newframe.setBounds(bounds);
1042         if (featureSettings != null && featureSettings.isShowing())
1043         {
1044           final Rectangle fspos = featureSettings.frame.getBounds();
1045           // TODO: need a 'show feature settings' function that takes bounds -
1046           // need to refactor Desktop.addFrame
1047           newframe.featureSettings_actionPerformed(null);
1048           final FeatureSettings nfs = newframe.featureSettings;
1049           SwingUtilities.invokeLater(new Runnable()
1050           {
1051             @Override
1052             public void run()
1053             {
1054               nfs.frame.setBounds(fspos);
1055             }
1056           });
1057           this.featureSettings.close();
1058           this.featureSettings = null;
1059         }
1060         this.closeMenuItem_actionPerformed(true);
1061       }
1062     }
1063   }
1064
1065   @Override
1066   public void addFromText_actionPerformed(ActionEvent e)
1067   {
1068     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1069             .getAlignPanel());
1070   }
1071
1072   @Override
1073   public void addFromURL_actionPerformed(ActionEvent e)
1074   {
1075     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1076   }
1077
1078   @Override
1079   public void save_actionPerformed(ActionEvent e)
1080   {
1081     if (fileName == null
1082             || (currentFileFormat == null || !jalview.io.FormatAdapter
1083                     .isValidIOFormat(currentFileFormat, true))
1084             || fileName.startsWith("http"))
1085     {
1086       saveAs_actionPerformed(null);
1087     }
1088     else
1089     {
1090       saveAlignment(fileName, currentFileFormat);
1091     }
1092   }
1093
1094   /**
1095    * DOCUMENT ME!
1096    *
1097    * @param e
1098    *          DOCUMENT ME!
1099    */
1100   @Override
1101   public void saveAs_actionPerformed(ActionEvent e)
1102   {
1103     JalviewFileChooser chooser = new JalviewFileChooser(
1104             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1105             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1106             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1107             currentFileFormat, false);
1108
1109     chooser.setFileView(new JalviewFileView());
1110     chooser.setDialogTitle(MessageManager
1111             .getString("label.save_alignment_to_file"));
1112     chooser.setToolTipText(MessageManager.getString("action.save"));
1113
1114     int value = chooser.showSaveDialog(this);
1115
1116     if (value == JalviewFileChooser.APPROVE_OPTION)
1117     {
1118       currentFileFormat = chooser.getSelectedFormat();
1119       while (currentFileFormat == null)
1120       {
1121         JOptionPane
1122                 .showInternalMessageDialog(
1123                         Desktop.desktop,
1124                         MessageManager
1125                                 .getString("label.select_file_format_before_saving"),
1126                         MessageManager
1127                                 .getString("label.file_format_not_specified"),
1128                         JOptionPane.WARNING_MESSAGE);
1129         currentFileFormat = chooser.getSelectedFormat();
1130         value = chooser.showSaveDialog(this);
1131         if (value != JalviewFileChooser.APPROVE_OPTION)
1132         {
1133           return;
1134         }
1135       }
1136
1137       fileName = chooser.getSelectedFile().getPath();
1138
1139       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1140               currentFileFormat);
1141
1142       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1143       if (currentFileFormat.indexOf(" ") > -1)
1144       {
1145         currentFileFormat = currentFileFormat.substring(0,
1146                 currentFileFormat.indexOf(" "));
1147       }
1148       saveAlignment(fileName, currentFileFormat);
1149     }
1150   }
1151
1152   public boolean saveAlignment(String file, String format)
1153   {
1154     boolean success = true;
1155
1156     if (format.equalsIgnoreCase("Jalview"))
1157     {
1158       String shortName = title;
1159
1160       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161       {
1162         shortName = shortName.substring(shortName
1163                 .lastIndexOf(java.io.File.separatorChar) + 1);
1164       }
1165
1166       success = new Jalview2XML().saveAlignment(this, file, shortName);
1167
1168       statusBar.setText(MessageManager.formatMessage(
1169               "label.successfully_saved_to_file_in_format", new Object[] {
1170                   fileName, format }));
1171
1172     }
1173     else
1174     {
1175       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1176       {
1177         warningMessage("Cannot save file " + fileName + " using format "
1178                 + format, "Alignment output format not supported");
1179         if (!Jalview.isHeadlessMode())
1180         {
1181           saveAs_actionPerformed(null);
1182         }
1183         return false;
1184       }
1185
1186       AlignmentExportData exportData = getAlignmentForExport(format,
1187               viewport, null);
1188       if (exportData.getSettings().isCancelled())
1189       {
1190         return false;
1191       }
1192       FormatAdapter f = new FormatAdapter(alignPanel,
1193               exportData.getSettings());
1194       String output = f.formatSequences(
1195               format,
1196               exportData.getAlignment(), // class cast exceptions will
1197               // occur in the distant future
1198               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1199               f.getCacheSuffixDefault(format),
1200               viewport.getColumnSelection());
1201
1202       if (output == null)
1203       {
1204         success = false;
1205       }
1206       else
1207       {
1208         try
1209         {
1210           java.io.PrintWriter out = new java.io.PrintWriter(
1211                   new java.io.FileWriter(file));
1212
1213           out.print(output);
1214           out.close();
1215           this.setTitle(file);
1216           statusBar.setText(MessageManager.formatMessage(
1217                   "label.successfully_saved_to_file_in_format",
1218                   new Object[] { fileName, format }));
1219         } catch (Exception ex)
1220         {
1221           success = false;
1222           ex.printStackTrace();
1223         }
1224       }
1225     }
1226
1227     if (!success)
1228     {
1229       JOptionPane.showInternalMessageDialog(this, MessageManager
1230               .formatMessage("label.couldnt_save_file",
1231                       new Object[] { fileName }), MessageManager
1232               .getString("label.error_saving_file"),
1233               JOptionPane.WARNING_MESSAGE);
1234     }
1235
1236     return success;
1237   }
1238
1239   private void warningMessage(String warning, String title)
1240   {
1241     if (new jalview.util.Platform().isHeadless())
1242     {
1243       System.err.println("Warning: " + title + "\nWarning: " + warning);
1244
1245     }
1246     else
1247     {
1248       JOptionPane.showInternalMessageDialog(this, warning, title,
1249               JOptionPane.WARNING_MESSAGE);
1250     }
1251     return;
1252   }
1253
1254   /**
1255    * DOCUMENT ME!
1256    *
1257    * @param e
1258    *          DOCUMENT ME!
1259    */
1260   @Override
1261   protected void outputText_actionPerformed(ActionEvent e)
1262   {
1263
1264     AlignmentExportData exportData = getAlignmentForExport(
1265             e.getActionCommand(), viewport, null);
1266     if (exportData.getSettings().isCancelled())
1267     {
1268       return;
1269     }
1270     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1271     cap.setForInput(null);
1272     try
1273     {
1274       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1275               .formatSequences(e.getActionCommand(),
1276                       exportData.getAlignment(),
1277                       exportData.getOmitHidden(),
1278                       exportData.getStartEndPostions(),
1279                       viewport.getColumnSelection()));
1280       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1281               "label.alignment_output_command",
1282               new Object[] { e.getActionCommand() }), 600, 500);
1283     } catch (OutOfMemoryError oom)
1284     {
1285       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1286       cap.dispose();
1287     }
1288
1289   }
1290
1291   public static AlignmentExportData getAlignmentForExport(
1292           String exportFormat, AlignViewportI viewport,
1293           AlignExportSettingI exportSettings)
1294   {
1295     AlignmentI alignmentToExport = null;
1296     AlignExportSettingI settings = exportSettings;
1297     String[] omitHidden = null;
1298
1299     HiddenSequences hiddenSeqs = viewport.getAlignment()
1300             .getHiddenSequences();
1301
1302     alignmentToExport = viewport.getAlignment();
1303
1304     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1305     if (settings == null)
1306     {
1307       settings = new AlignExportSettings(hasHiddenSeqs,
1308               viewport.hasHiddenColumns(), exportFormat);
1309     }
1310     // settings.isExportAnnotations();
1311
1312     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1313     {
1314       omitHidden = viewport.getViewAsString(false,
1315               settings.isExportHiddenSequences());
1316     }
1317
1318     int[] alignmentStartEnd = new int[2];
1319     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1320     {
1321       alignmentToExport = hiddenSeqs.getFullAlignment();
1322     }
1323     else
1324     {
1325       alignmentToExport = viewport.getAlignment();
1326     }
1327     alignmentStartEnd = alignmentToExport
1328             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1329                     .getHiddenColumns());
1330     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1331             omitHidden, alignmentStartEnd, settings);
1332     return ed;
1333   }
1334
1335   /**
1336    * DOCUMENT ME!
1337    *
1338    * @param e
1339    *          DOCUMENT ME!
1340    */
1341   @Override
1342   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1343   {
1344     new HtmlSvgOutput(null, alignPanel);
1345   }
1346
1347   @Override
1348   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1349   {
1350     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1351     bjs.exportJalviewAlignmentAsBioJsHtmlFile(null);
1352   }
1353
1354   public void createImageMap(File file, String image)
1355   {
1356     alignPanel.makePNGImageMap(file, image);
1357   }
1358
1359   /**
1360    * DOCUMENT ME!
1361    *
1362    * @param e
1363    *          DOCUMENT ME!
1364    */
1365   @Override
1366   public void createPNG(File f)
1367   {
1368     alignPanel.makePNG(f);
1369   }
1370
1371   /**
1372    * DOCUMENT ME!
1373    *
1374    * @param e
1375    *          DOCUMENT ME!
1376    */
1377   @Override
1378   public void createEPS(File f)
1379   {
1380     alignPanel.makeEPS(f);
1381   }
1382
1383   @Override
1384   public void createSVG(File f)
1385   {
1386     alignPanel.makeSVG(f);
1387   }
1388
1389   @Override
1390   public void pageSetup_actionPerformed(ActionEvent e)
1391   {
1392     PrinterJob printJob = PrinterJob.getPrinterJob();
1393     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1394   }
1395
1396   /**
1397    * DOCUMENT ME!
1398    *
1399    * @param e
1400    *          DOCUMENT ME!
1401    */
1402   @Override
1403   public void printMenuItem_actionPerformed(ActionEvent e)
1404   {
1405     // Putting in a thread avoids Swing painting problems
1406     PrintThread thread = new PrintThread(alignPanel);
1407     thread.start();
1408   }
1409
1410   @Override
1411   public void exportFeatures_actionPerformed(ActionEvent e)
1412   {
1413     new AnnotationExporter().exportFeatures(alignPanel);
1414   }
1415
1416   @Override
1417   public void exportAnnotations_actionPerformed(ActionEvent e)
1418   {
1419     new AnnotationExporter().exportAnnotations(alignPanel);
1420   }
1421
1422   @Override
1423   public void associatedData_actionPerformed(ActionEvent e)
1424   {
1425     // Pick the tree file
1426     JalviewFileChooser chooser = new JalviewFileChooser(
1427             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1428     chooser.setFileView(new JalviewFileView());
1429     chooser.setDialogTitle(MessageManager
1430             .getString("label.load_jalview_annotations"));
1431     chooser.setToolTipText(MessageManager
1432             .getString("label.load_jalview_annotations"));
1433
1434     int value = chooser.showOpenDialog(null);
1435
1436     if (value == JalviewFileChooser.APPROVE_OPTION)
1437     {
1438       String choice = chooser.getSelectedFile().getPath();
1439       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1440       loadJalviewDataFile(choice, null, null, null);
1441     }
1442
1443   }
1444
1445   /**
1446    * Close the current view or all views in the alignment frame. If the frame
1447    * only contains one view then the alignment will be removed from memory.
1448    *
1449    * @param closeAllTabs
1450    */
1451   @Override
1452   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1453   {
1454     if (alignPanels != null && alignPanels.size() < 2)
1455     {
1456       closeAllTabs = true;
1457     }
1458
1459     try
1460     {
1461       if (alignPanels != null)
1462       {
1463         if (closeAllTabs)
1464         {
1465           if (this.isClosed())
1466           {
1467             // really close all the windows - otherwise wait till
1468             // setClosed(true) is called
1469             for (int i = 0; i < alignPanels.size(); i++)
1470             {
1471               AlignmentPanel ap = alignPanels.get(i);
1472               ap.closePanel();
1473             }
1474           }
1475         }
1476         else
1477         {
1478           closeView(alignPanel);
1479         }
1480       }
1481
1482       if (closeAllTabs)
1483       {
1484         /*
1485          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1486          * be called recursively, with the frame now in 'closed' state
1487          */
1488         this.setClosed(true);
1489       }
1490     } catch (Exception ex)
1491     {
1492       ex.printStackTrace();
1493     }
1494   }
1495
1496   /**
1497    * Close the specified panel and close up tabs appropriately.
1498    *
1499    * @param panelToClose
1500    */
1501   public void closeView(AlignmentPanel panelToClose)
1502   {
1503     int index = tabbedPane.getSelectedIndex();
1504     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1505     alignPanels.remove(panelToClose);
1506     panelToClose.closePanel();
1507     panelToClose = null;
1508
1509     tabbedPane.removeTabAt(closedindex);
1510     tabbedPane.validate();
1511
1512     if (index > closedindex || index == tabbedPane.getTabCount())
1513     {
1514       // modify currently selected tab index if necessary.
1515       index--;
1516     }
1517
1518     this.tabSelectionChanged(index);
1519   }
1520
1521   /**
1522    * DOCUMENT ME!
1523    */
1524   void updateEditMenuBar()
1525   {
1526
1527     if (viewport.getHistoryList().size() > 0)
1528     {
1529       undoMenuItem.setEnabled(true);
1530       CommandI command = viewport.getHistoryList().peek();
1531       undoMenuItem.setText(MessageManager.formatMessage(
1532               "label.undo_command",
1533               new Object[] { command.getDescription() }));
1534     }
1535     else
1536     {
1537       undoMenuItem.setEnabled(false);
1538       undoMenuItem.setText(MessageManager.getString("action.undo"));
1539     }
1540
1541     if (viewport.getRedoList().size() > 0)
1542     {
1543       redoMenuItem.setEnabled(true);
1544
1545       CommandI command = viewport.getRedoList().peek();
1546       redoMenuItem.setText(MessageManager.formatMessage(
1547               "label.redo_command",
1548               new Object[] { command.getDescription() }));
1549     }
1550     else
1551     {
1552       redoMenuItem.setEnabled(false);
1553       redoMenuItem.setText(MessageManager.getString("action.redo"));
1554     }
1555   }
1556
1557   @Override
1558   public void addHistoryItem(CommandI command)
1559   {
1560     if (command.getSize() > 0)
1561     {
1562       viewport.addToHistoryList(command);
1563       viewport.clearRedoList();
1564       updateEditMenuBar();
1565       viewport.updateHiddenColumns();
1566       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1567       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1568       // viewport.getColumnSelection()
1569       // .getHiddenColumns().size() > 0);
1570     }
1571   }
1572
1573   /**
1574    *
1575    * @return alignment objects for all views
1576    */
1577   AlignmentI[] getViewAlignments()
1578   {
1579     if (alignPanels != null)
1580     {
1581       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1582       int i = 0;
1583       for (AlignmentPanel ap : alignPanels)
1584       {
1585         als[i++] = ap.av.getAlignment();
1586       }
1587       return als;
1588     }
1589     if (viewport != null)
1590     {
1591       return new AlignmentI[] { viewport.getAlignment() };
1592     }
1593     return null;
1594   }
1595
1596   /**
1597    * DOCUMENT ME!
1598    *
1599    * @param e
1600    *          DOCUMENT ME!
1601    */
1602   @Override
1603   protected void undoMenuItem_actionPerformed(ActionEvent e)
1604   {
1605     if (viewport.getHistoryList().isEmpty())
1606     {
1607       return;
1608     }
1609     CommandI command = viewport.getHistoryList().pop();
1610     viewport.addToRedoList(command);
1611     command.undoCommand(getViewAlignments());
1612
1613     AlignmentViewport originalSource = getOriginatingSource(command);
1614     updateEditMenuBar();
1615
1616     if (originalSource != null)
1617     {
1618       if (originalSource != viewport)
1619       {
1620         Cache.log
1621                 .warn("Implementation worry: mismatch of viewport origin for undo");
1622       }
1623       originalSource.updateHiddenColumns();
1624       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1625       // null
1626       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1627       // viewport.getColumnSelection()
1628       // .getHiddenColumns().size() > 0);
1629       originalSource.firePropertyChange("alignment", null, originalSource
1630               .getAlignment().getSequences());
1631     }
1632   }
1633
1634   /**
1635    * DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   @Override
1641   protected void redoMenuItem_actionPerformed(ActionEvent e)
1642   {
1643     if (viewport.getRedoList().size() < 1)
1644     {
1645       return;
1646     }
1647
1648     CommandI command = viewport.getRedoList().pop();
1649     viewport.addToHistoryList(command);
1650     command.doCommand(getViewAlignments());
1651
1652     AlignmentViewport originalSource = getOriginatingSource(command);
1653     updateEditMenuBar();
1654
1655     if (originalSource != null)
1656     {
1657
1658       if (originalSource != viewport)
1659       {
1660         Cache.log
1661                 .warn("Implementation worry: mismatch of viewport origin for redo");
1662       }
1663       originalSource.updateHiddenColumns();
1664       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1665       // null
1666       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1667       // viewport.getColumnSelection()
1668       // .getHiddenColumns().size() > 0);
1669       originalSource.firePropertyChange("alignment", null, originalSource
1670               .getAlignment().getSequences());
1671     }
1672   }
1673
1674   AlignmentViewport getOriginatingSource(CommandI command)
1675   {
1676     AlignmentViewport originalSource = null;
1677     // For sequence removal and addition, we need to fire
1678     // the property change event FROM the viewport where the
1679     // original alignment was altered
1680     AlignmentI al = null;
1681     if (command instanceof EditCommand)
1682     {
1683       EditCommand editCommand = (EditCommand) command;
1684       al = editCommand.getAlignment();
1685       List<Component> comps = PaintRefresher.components.get(viewport
1686               .getSequenceSetId());
1687
1688       for (Component comp : comps)
1689       {
1690         if (comp instanceof AlignmentPanel)
1691         {
1692           if (al == ((AlignmentPanel) comp).av.getAlignment())
1693           {
1694             originalSource = ((AlignmentPanel) comp).av;
1695             break;
1696           }
1697         }
1698       }
1699     }
1700
1701     if (originalSource == null)
1702     {
1703       // The original view is closed, we must validate
1704       // the current view against the closed view first
1705       if (al != null)
1706       {
1707         PaintRefresher.validateSequences(al, viewport.getAlignment());
1708       }
1709
1710       originalSource = viewport;
1711     }
1712
1713     return originalSource;
1714   }
1715
1716   /**
1717    * DOCUMENT ME!
1718    *
1719    * @param up
1720    *          DOCUMENT ME!
1721    */
1722   public void moveSelectedSequences(boolean up)
1723   {
1724     SequenceGroup sg = viewport.getSelectionGroup();
1725
1726     if (sg == null)
1727     {
1728       return;
1729     }
1730     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1731             viewport.getHiddenRepSequences(), up);
1732     alignPanel.paintAlignment(true);
1733   }
1734
1735   synchronized void slideSequences(boolean right, int size)
1736   {
1737     List<SequenceI> sg = new ArrayList<SequenceI>();
1738     if (viewport.cursorMode)
1739     {
1740       sg.add(viewport.getAlignment().getSequenceAt(
1741               alignPanel.getSeqPanel().seqCanvas.cursorY));
1742     }
1743     else if (viewport.getSelectionGroup() != null
1744             && viewport.getSelectionGroup().getSize() != viewport
1745                     .getAlignment().getHeight())
1746     {
1747       sg = viewport.getSelectionGroup().getSequences(
1748               viewport.getHiddenRepSequences());
1749     }
1750
1751     if (sg.size() < 1)
1752     {
1753       return;
1754     }
1755
1756     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1757
1758     for (SequenceI seq : viewport.getAlignment().getSequences())
1759     {
1760       if (!sg.contains(seq))
1761       {
1762         invertGroup.add(seq);
1763       }
1764     }
1765
1766     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1767
1768     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1769     for (int i = 0; i < invertGroup.size(); i++)
1770     {
1771       seqs2[i] = invertGroup.get(i);
1772     }
1773
1774     SlideSequencesCommand ssc;
1775     if (right)
1776     {
1777       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1778               size, viewport.getGapCharacter());
1779     }
1780     else
1781     {
1782       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1783               size, viewport.getGapCharacter());
1784     }
1785
1786     int groupAdjustment = 0;
1787     if (ssc.getGapsInsertedBegin() && right)
1788     {
1789       if (viewport.cursorMode)
1790       {
1791         alignPanel.getSeqPanel().moveCursor(size, 0);
1792       }
1793       else
1794       {
1795         groupAdjustment = size;
1796       }
1797     }
1798     else if (!ssc.getGapsInsertedBegin() && !right)
1799     {
1800       if (viewport.cursorMode)
1801       {
1802         alignPanel.getSeqPanel().moveCursor(-size, 0);
1803       }
1804       else
1805       {
1806         groupAdjustment = -size;
1807       }
1808     }
1809
1810     if (groupAdjustment != 0)
1811     {
1812       viewport.getSelectionGroup().setStartRes(
1813               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1814       viewport.getSelectionGroup().setEndRes(
1815               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1816     }
1817
1818     /*
1819      * just extend the last slide command if compatible; but not if in
1820      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1821      */
1822     boolean appendHistoryItem = false;
1823     Deque<CommandI> historyList = viewport.getHistoryList();
1824     boolean inSplitFrame = getSplitViewContainer() != null;
1825     if (!inSplitFrame && historyList != null && historyList.size() > 0
1826             && historyList.peek() instanceof SlideSequencesCommand)
1827     {
1828       appendHistoryItem = ssc
1829               .appendSlideCommand((SlideSequencesCommand) historyList
1830                       .peek());
1831     }
1832
1833     if (!appendHistoryItem)
1834     {
1835       addHistoryItem(ssc);
1836     }
1837
1838     repaint();
1839   }
1840
1841   /**
1842    * DOCUMENT ME!
1843    *
1844    * @param e
1845    *          DOCUMENT ME!
1846    */
1847   @Override
1848   protected void copy_actionPerformed(ActionEvent e)
1849   {
1850     System.gc();
1851     if (viewport.getSelectionGroup() == null)
1852     {
1853       return;
1854     }
1855     // TODO: preserve the ordering of displayed alignment annotation in any
1856     // internal paste (particularly sequence associated annotation)
1857     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1858     String[] omitHidden = null;
1859
1860     if (viewport.hasHiddenColumns())
1861     {
1862       omitHidden = viewport.getViewAsString(true);
1863     }
1864
1865     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1866             omitHidden, null);
1867
1868     StringSelection ss = new StringSelection(output);
1869
1870     try
1871     {
1872       jalview.gui.Desktop.internalCopy = true;
1873       // Its really worth setting the clipboard contents
1874       // to empty before setting the large StringSelection!!
1875       Toolkit.getDefaultToolkit().getSystemClipboard()
1876               .setContents(new StringSelection(""), null);
1877
1878       Toolkit.getDefaultToolkit().getSystemClipboard()
1879               .setContents(ss, Desktop.instance);
1880     } catch (OutOfMemoryError er)
1881     {
1882       new OOMWarning("copying region", er);
1883       return;
1884     }
1885
1886     ArrayList<int[]> hiddenColumns = null;
1887     if (viewport.hasHiddenColumns())
1888     {
1889       hiddenColumns = new ArrayList<int[]>();
1890       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1891               .getSelectionGroup().getEndRes();
1892       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1893       {
1894         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1895         {
1896           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1897               region[1] - hiddenOffset });
1898         }
1899       }
1900     }
1901
1902     Desktop.jalviewClipboard = new Object[] { seqs,
1903         viewport.getAlignment().getDataset(), hiddenColumns };
1904     statusBar.setText(MessageManager.formatMessage(
1905             "label.copied_sequences_to_clipboard", new Object[] { Integer
1906                     .valueOf(seqs.length).toString() }));
1907   }
1908
1909   /**
1910    * DOCUMENT ME!
1911    *
1912    * @param e
1913    *          DOCUMENT ME!
1914    */
1915   @Override
1916   protected void pasteNew_actionPerformed(ActionEvent e)
1917   {
1918     paste(true);
1919   }
1920
1921   /**
1922    * DOCUMENT ME!
1923    *
1924    * @param e
1925    *          DOCUMENT ME!
1926    */
1927   @Override
1928   protected void pasteThis_actionPerformed(ActionEvent e)
1929   {
1930     paste(false);
1931   }
1932
1933   /**
1934    * Paste contents of Jalview clipboard
1935    *
1936    * @param newAlignment
1937    *          true to paste to a new alignment, otherwise add to this.
1938    */
1939   void paste(boolean newAlignment)
1940   {
1941     boolean externalPaste = true;
1942     try
1943     {
1944       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1945       Transferable contents = c.getContents(this);
1946
1947       if (contents == null)
1948       {
1949         return;
1950       }
1951
1952       String str, format;
1953       try
1954       {
1955         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1956         if (str.length() < 1)
1957         {
1958           return;
1959         }
1960
1961         format = new IdentifyFile().identify(str, "Paste");
1962
1963       } catch (OutOfMemoryError er)
1964       {
1965         new OOMWarning("Out of memory pasting sequences!!", er);
1966         return;
1967       }
1968
1969       SequenceI[] sequences;
1970       boolean annotationAdded = false;
1971       AlignmentI alignment = null;
1972
1973       if (Desktop.jalviewClipboard != null)
1974       {
1975         // The clipboard was filled from within Jalview, we must use the
1976         // sequences
1977         // And dataset from the copied alignment
1978         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1979         // be doubly sure that we create *new* sequence objects.
1980         sequences = new SequenceI[newseq.length];
1981         for (int i = 0; i < newseq.length; i++)
1982         {
1983           sequences[i] = new Sequence(newseq[i]);
1984         }
1985         alignment = new Alignment(sequences);
1986         externalPaste = false;
1987       }
1988       else
1989       {
1990         // parse the clipboard as an alignment.
1991         alignment = new FormatAdapter().readFile(str, "Paste", format);
1992         sequences = alignment.getSequencesArray();
1993       }
1994
1995       int alwidth = 0;
1996       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1997       int fgroup = -1;
1998
1999       if (newAlignment)
2000       {
2001
2002         if (Desktop.jalviewClipboard != null)
2003         {
2004           // dataset is inherited
2005           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2006         }
2007         else
2008         {
2009           // new dataset is constructed
2010           alignment.setDataset(null);
2011         }
2012         alwidth = alignment.getWidth() + 1;
2013       }
2014       else
2015       {
2016         AlignmentI pastedal = alignment; // preserve pasted alignment object
2017         // Add pasted sequences and dataset into existing alignment.
2018         alignment = viewport.getAlignment();
2019         alwidth = alignment.getWidth() + 1;
2020         // decide if we need to import sequences from an existing dataset
2021         boolean importDs = Desktop.jalviewClipboard != null
2022                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2023         // importDs==true instructs us to copy over new dataset sequences from
2024         // an existing alignment
2025         Vector newDs = (importDs) ? new Vector() : null; // used to create
2026         // minimum dataset set
2027
2028         for (int i = 0; i < sequences.length; i++)
2029         {
2030           if (importDs)
2031           {
2032             newDs.addElement(null);
2033           }
2034           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2035           // paste
2036           if (importDs && ds != null)
2037           {
2038             if (!newDs.contains(ds))
2039             {
2040               newDs.setElementAt(ds, i);
2041               ds = new Sequence(ds);
2042               // update with new dataset sequence
2043               sequences[i].setDatasetSequence(ds);
2044             }
2045             else
2046             {
2047               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2048             }
2049           }
2050           else
2051           {
2052             // copy and derive new dataset sequence
2053             sequences[i] = sequences[i].deriveSequence();
2054             alignment.getDataset().addSequence(
2055                     sequences[i].getDatasetSequence());
2056             // TODO: avoid creation of duplicate dataset sequences with a
2057             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2058           }
2059           alignment.addSequence(sequences[i]); // merges dataset
2060         }
2061         if (newDs != null)
2062         {
2063           newDs.clear(); // tidy up
2064         }
2065         if (alignment.getAlignmentAnnotation() != null)
2066         {
2067           for (AlignmentAnnotation alan : alignment
2068                   .getAlignmentAnnotation())
2069           {
2070             if (alan.graphGroup > fgroup)
2071             {
2072               fgroup = alan.graphGroup;
2073             }
2074           }
2075         }
2076         if (pastedal.getAlignmentAnnotation() != null)
2077         {
2078           // Add any annotation attached to alignment.
2079           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2080           for (int i = 0; i < alann.length; i++)
2081           {
2082             annotationAdded = true;
2083             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2084             {
2085               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2086               if (newann.graphGroup > -1)
2087               {
2088                 if (newGraphGroups.size() <= newann.graphGroup
2089                         || newGraphGroups.get(newann.graphGroup) == null)
2090                 {
2091                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2092                   {
2093                     newGraphGroups.add(q, null);
2094                   }
2095                   newGraphGroups.set(newann.graphGroup, new Integer(
2096                           ++fgroup));
2097                 }
2098                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2099                         .intValue();
2100               }
2101
2102               newann.padAnnotation(alwidth);
2103               alignment.addAnnotation(newann);
2104             }
2105           }
2106         }
2107       }
2108       if (!newAlignment)
2109       {
2110         // /////
2111         // ADD HISTORY ITEM
2112         //
2113         addHistoryItem(new EditCommand(
2114                 MessageManager.getString("label.add_sequences"),
2115                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2116       }
2117       // Add any annotations attached to sequences
2118       for (int i = 0; i < sequences.length; i++)
2119       {
2120         if (sequences[i].getAnnotation() != null)
2121         {
2122           AlignmentAnnotation newann;
2123           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2124           {
2125             annotationAdded = true;
2126             newann = sequences[i].getAnnotation()[a];
2127             newann.adjustForAlignment();
2128             newann.padAnnotation(alwidth);
2129             if (newann.graphGroup > -1)
2130             {
2131               if (newann.graphGroup > -1)
2132               {
2133                 if (newGraphGroups.size() <= newann.graphGroup
2134                         || newGraphGroups.get(newann.graphGroup) == null)
2135                 {
2136                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2137                   {
2138                     newGraphGroups.add(q, null);
2139                   }
2140                   newGraphGroups.set(newann.graphGroup, new Integer(
2141                           ++fgroup));
2142                 }
2143                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2144                         .intValue();
2145               }
2146             }
2147             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2148             // was
2149             // duplicated
2150             // earlier
2151             alignment
2152                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2153           }
2154         }
2155       }
2156       if (!newAlignment)
2157       {
2158
2159         // propagate alignment changed.
2160         viewport.setEndSeq(alignment.getHeight());
2161         if (annotationAdded)
2162         {
2163           // Duplicate sequence annotation in all views.
2164           AlignmentI[] alview = this.getViewAlignments();
2165           for (int i = 0; i < sequences.length; i++)
2166           {
2167             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2168             if (sann == null)
2169             {
2170               continue;
2171             }
2172             for (int avnum = 0; avnum < alview.length; avnum++)
2173             {
2174               if (alview[avnum] != alignment)
2175               {
2176                 // duplicate in a view other than the one with input focus
2177                 int avwidth = alview[avnum].getWidth() + 1;
2178                 // this relies on sann being preserved after we
2179                 // modify the sequence's annotation array for each duplication
2180                 for (int a = 0; a < sann.length; a++)
2181                 {
2182                   AlignmentAnnotation newann = new AlignmentAnnotation(
2183                           sann[a]);
2184                   sequences[i].addAlignmentAnnotation(newann);
2185                   newann.padAnnotation(avwidth);
2186                   alview[avnum].addAnnotation(newann); // annotation was
2187                   // duplicated earlier
2188                   // TODO JAL-1145 graphGroups are not updated for sequence
2189                   // annotation added to several views. This may cause
2190                   // strangeness
2191                   alview[avnum].setAnnotationIndex(newann, a);
2192                 }
2193               }
2194             }
2195           }
2196           buildSortByAnnotationScoresMenu();
2197         }
2198         viewport.firePropertyChange("alignment", null,
2199                 alignment.getSequences());
2200         if (alignPanels != null)
2201         {
2202           for (AlignmentPanel ap : alignPanels)
2203           {
2204             ap.validateAnnotationDimensions(false);
2205           }
2206         }
2207         else
2208         {
2209           alignPanel.validateAnnotationDimensions(false);
2210         }
2211
2212       }
2213       else
2214       {
2215         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2216                 DEFAULT_HEIGHT);
2217         String newtitle = new String("Copied sequences");
2218
2219         if (Desktop.jalviewClipboard != null
2220                 && Desktop.jalviewClipboard[2] != null)
2221         {
2222           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2223           for (int[] region : hc)
2224           {
2225             af.viewport.hideColumns(region[0], region[1]);
2226           }
2227         }
2228
2229         // >>>This is a fix for the moment, until a better solution is
2230         // found!!<<<
2231         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2232                 .transferSettings(
2233                         alignPanel.getSeqPanel().seqCanvas
2234                                 .getFeatureRenderer());
2235
2236         // TODO: maintain provenance of an alignment, rather than just make the
2237         // title a concatenation of operations.
2238         if (!externalPaste)
2239         {
2240           if (title.startsWith("Copied sequences"))
2241           {
2242             newtitle = title;
2243           }
2244           else
2245           {
2246             newtitle = newtitle.concat("- from " + title);
2247           }
2248         }
2249         else
2250         {
2251           newtitle = new String("Pasted sequences");
2252         }
2253
2254         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2255                 DEFAULT_HEIGHT);
2256
2257       }
2258
2259     } catch (Exception ex)
2260     {
2261       ex.printStackTrace();
2262       System.out.println("Exception whilst pasting: " + ex);
2263       // could be anything being pasted in here
2264     }
2265
2266   }
2267
2268   @Override
2269   protected void expand_newalign(ActionEvent e)
2270   {
2271     try
2272     {
2273       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2274               .getAlignment(), -1);
2275       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2276               DEFAULT_HEIGHT);
2277       String newtitle = new String("Flanking alignment");
2278
2279       if (Desktop.jalviewClipboard != null
2280               && Desktop.jalviewClipboard[2] != null)
2281       {
2282         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2283         for (int region[] : hc)
2284         {
2285           af.viewport.hideColumns(region[0], region[1]);
2286         }
2287       }
2288
2289       // >>>This is a fix for the moment, until a better solution is
2290       // found!!<<<
2291       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2292               .transferSettings(
2293                       alignPanel.getSeqPanel().seqCanvas
2294                               .getFeatureRenderer());
2295
2296       // TODO: maintain provenance of an alignment, rather than just make the
2297       // title a concatenation of operations.
2298       {
2299         if (title.startsWith("Copied sequences"))
2300         {
2301           newtitle = title;
2302         }
2303         else
2304         {
2305           newtitle = newtitle.concat("- from " + title);
2306         }
2307       }
2308
2309       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2310
2311     } catch (Exception ex)
2312     {
2313       ex.printStackTrace();
2314       System.out.println("Exception whilst pasting: " + ex);
2315       // could be anything being pasted in here
2316     } catch (OutOfMemoryError oom)
2317     {
2318       new OOMWarning("Viewing flanking region of alignment", oom);
2319     }
2320   }
2321
2322   /**
2323    * DOCUMENT ME!
2324    *
2325    * @param e
2326    *          DOCUMENT ME!
2327    */
2328   @Override
2329   protected void cut_actionPerformed(ActionEvent e)
2330   {
2331     copy_actionPerformed(null);
2332     delete_actionPerformed(null);
2333   }
2334
2335   /**
2336    * DOCUMENT ME!
2337    *
2338    * @param e
2339    *          DOCUMENT ME!
2340    */
2341   @Override
2342   protected void delete_actionPerformed(ActionEvent evt)
2343   {
2344
2345     SequenceGroup sg = viewport.getSelectionGroup();
2346     if (sg == null)
2347     {
2348       return;
2349     }
2350
2351     /*
2352      * If the cut affects all sequences, warn, remove highlighted columns
2353      */
2354     if (sg.getSize() == viewport.getAlignment().getHeight())
2355     {
2356       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2357               .getAlignment().getWidth()) ? true : false;
2358       if (isEntireAlignWidth)
2359       {
2360         int confirm = JOptionPane.showConfirmDialog(this,
2361                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2362                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2363                 JOptionPane.OK_CANCEL_OPTION);
2364
2365         if (confirm == JOptionPane.CANCEL_OPTION
2366                 || confirm == JOptionPane.CLOSED_OPTION)
2367         {
2368           return;
2369         }
2370       }
2371       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2372               sg.getEndRes() + 1);
2373     }
2374     SequenceI[] cut = sg.getSequences()
2375             .toArray(new SequenceI[sg.getSize()]);
2376
2377     addHistoryItem(new EditCommand(
2378             MessageManager.getString("label.cut_sequences"), Action.CUT,
2379             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2380             viewport.getAlignment()));
2381
2382     viewport.setSelectionGroup(null);
2383     viewport.sendSelection();
2384     viewport.getAlignment().deleteGroup(sg);
2385
2386     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2387             .getSequences());
2388     if (viewport.getAlignment().getHeight() < 1)
2389     {
2390       try
2391       {
2392         this.setClosed(true);
2393       } catch (Exception ex)
2394       {
2395       }
2396     }
2397   }
2398
2399   /**
2400    * DOCUMENT ME!
2401    *
2402    * @param e
2403    *          DOCUMENT ME!
2404    */
2405   @Override
2406   protected void deleteGroups_actionPerformed(ActionEvent e)
2407   {
2408     if (avc.deleteGroups())
2409     {
2410       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2411       alignPanel.updateAnnotation();
2412       alignPanel.paintAlignment(true);
2413     }
2414   }
2415
2416   /**
2417    * DOCUMENT ME!
2418    *
2419    * @param e
2420    *          DOCUMENT ME!
2421    */
2422   @Override
2423   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2424   {
2425     SequenceGroup sg = new SequenceGroup();
2426
2427     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2428     {
2429       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2430     }
2431
2432     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2433     viewport.setSelectionGroup(sg);
2434     viewport.sendSelection();
2435     // JAL-2034 - should delegate to
2436     // alignPanel to decide if overview needs
2437     // updating.
2438     alignPanel.paintAlignment(false);
2439     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2440   }
2441
2442   /**
2443    * DOCUMENT ME!
2444    *
2445    * @param e
2446    *          DOCUMENT ME!
2447    */
2448   @Override
2449   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2450   {
2451     if (viewport.cursorMode)
2452     {
2453       alignPanel.getSeqPanel().keyboardNo1 = null;
2454       alignPanel.getSeqPanel().keyboardNo2 = null;
2455     }
2456     viewport.setSelectionGroup(null);
2457     viewport.getColumnSelection().clear();
2458     viewport.setSelectionGroup(null);
2459     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2460     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2461     // JAL-2034 - should delegate to
2462     // alignPanel to decide if overview needs
2463     // updating.
2464     alignPanel.paintAlignment(false);
2465     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466     viewport.sendSelection();
2467   }
2468
2469   /**
2470    * DOCUMENT ME!
2471    *
2472    * @param e
2473    *          DOCUMENT ME!
2474    */
2475   @Override
2476   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2477   {
2478     SequenceGroup sg = viewport.getSelectionGroup();
2479
2480     if (sg == null)
2481     {
2482       selectAllSequenceMenuItem_actionPerformed(null);
2483
2484       return;
2485     }
2486
2487     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2488     {
2489       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2490     }
2491     // JAL-2034 - should delegate to
2492     // alignPanel to decide if overview needs
2493     // updating.
2494
2495     alignPanel.paintAlignment(true);
2496     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2497     viewport.sendSelection();
2498   }
2499
2500   @Override
2501   public void invertColSel_actionPerformed(ActionEvent e)
2502   {
2503     viewport.invertColumnSelection();
2504     alignPanel.paintAlignment(true);
2505     viewport.sendSelection();
2506   }
2507
2508   /**
2509    * DOCUMENT ME!
2510    *
2511    * @param e
2512    *          DOCUMENT ME!
2513    */
2514   @Override
2515   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2516   {
2517     trimAlignment(true);
2518   }
2519
2520   /**
2521    * DOCUMENT ME!
2522    *
2523    * @param e
2524    *          DOCUMENT ME!
2525    */
2526   @Override
2527   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2528   {
2529     trimAlignment(false);
2530   }
2531
2532   void trimAlignment(boolean trimLeft)
2533   {
2534     ColumnSelection colSel = viewport.getColumnSelection();
2535     int column;
2536
2537     if (!colSel.isEmpty())
2538     {
2539       if (trimLeft)
2540       {
2541         column = colSel.getMin();
2542       }
2543       else
2544       {
2545         column = colSel.getMax();
2546       }
2547
2548       SequenceI[] seqs;
2549       if (viewport.getSelectionGroup() != null)
2550       {
2551         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2552                 viewport.getHiddenRepSequences());
2553       }
2554       else
2555       {
2556         seqs = viewport.getAlignment().getSequencesArray();
2557       }
2558
2559       TrimRegionCommand trimRegion;
2560       if (trimLeft)
2561       {
2562         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2563                 column, viewport.getAlignment());
2564         viewport.setStartRes(0);
2565       }
2566       else
2567       {
2568         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2569                 column, viewport.getAlignment());
2570       }
2571
2572       statusBar.setText(MessageManager.formatMessage(
2573               "label.removed_columns",
2574               new String[] { Integer.valueOf(trimRegion.getSize())
2575                       .toString() }));
2576
2577       addHistoryItem(trimRegion);
2578
2579       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2580       {
2581         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2582                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2583         {
2584           viewport.getAlignment().deleteGroup(sg);
2585         }
2586       }
2587
2588       viewport.firePropertyChange("alignment", null, viewport
2589               .getAlignment().getSequences());
2590     }
2591   }
2592
2593   /**
2594    * DOCUMENT ME!
2595    *
2596    * @param e
2597    *          DOCUMENT ME!
2598    */
2599   @Override
2600   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2601   {
2602     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2603
2604     SequenceI[] seqs;
2605     if (viewport.getSelectionGroup() != null)
2606     {
2607       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2608               viewport.getHiddenRepSequences());
2609       start = viewport.getSelectionGroup().getStartRes();
2610       end = viewport.getSelectionGroup().getEndRes();
2611     }
2612     else
2613     {
2614       seqs = viewport.getAlignment().getSequencesArray();
2615     }
2616
2617     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2618             "Remove Gapped Columns", seqs, start, end,
2619             viewport.getAlignment());
2620
2621     addHistoryItem(removeGapCols);
2622
2623     statusBar.setText(MessageManager.formatMessage(
2624             "label.removed_empty_columns",
2625             new Object[] { Integer.valueOf(removeGapCols.getSize())
2626                     .toString() }));
2627
2628     // This is to maintain viewport position on first residue
2629     // of first sequence
2630     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2631     int startRes = seq.findPosition(viewport.startRes);
2632     // ShiftList shifts;
2633     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2634     // edit.alColumnChanges=shifts.getInverse();
2635     // if (viewport.hasHiddenColumns)
2636     // viewport.getColumnSelection().compensateForEdits(shifts);
2637     viewport.setStartRes(seq.findIndex(startRes) - 1);
2638     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2639             .getSequences());
2640
2641   }
2642
2643   /**
2644    * DOCUMENT ME!
2645    *
2646    * @param e
2647    *          DOCUMENT ME!
2648    */
2649   @Override
2650   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2651   {
2652     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2653
2654     SequenceI[] seqs;
2655     if (viewport.getSelectionGroup() != null)
2656     {
2657       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2658               viewport.getHiddenRepSequences());
2659       start = viewport.getSelectionGroup().getStartRes();
2660       end = viewport.getSelectionGroup().getEndRes();
2661     }
2662     else
2663     {
2664       seqs = viewport.getAlignment().getSequencesArray();
2665     }
2666
2667     // This is to maintain viewport position on first residue
2668     // of first sequence
2669     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2670     int startRes = seq.findPosition(viewport.startRes);
2671
2672     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2673             viewport.getAlignment()));
2674
2675     viewport.setStartRes(seq.findIndex(startRes) - 1);
2676
2677     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2678             .getSequences());
2679
2680   }
2681
2682   /**
2683    * DOCUMENT ME!
2684    *
2685    * @param e
2686    *          DOCUMENT ME!
2687    */
2688   @Override
2689   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2690   {
2691     viewport.setPadGaps(padGapsMenuitem.isSelected());
2692     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2693             .getSequences());
2694   }
2695
2696   /**
2697    * DOCUMENT ME!
2698    *
2699    * @param e
2700    *          DOCUMENT ME!
2701    */
2702   @Override
2703   public void findMenuItem_actionPerformed(ActionEvent e)
2704   {
2705     new Finder();
2706   }
2707
2708   /**
2709    * Create a new view of the current alignment.
2710    */
2711   @Override
2712   public void newView_actionPerformed(ActionEvent e)
2713   {
2714     newView(null, true);
2715   }
2716
2717   /**
2718    * Creates and shows a new view of the current alignment.
2719    *
2720    * @param viewTitle
2721    *          title of newly created view; if null, one will be generated
2722    * @param copyAnnotation
2723    *          if true then duplicate all annnotation, groups and settings
2724    * @return new alignment panel, already displayed.
2725    */
2726   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2727   {
2728     /*
2729      * Create a new AlignmentPanel (with its own, new Viewport)
2730      */
2731     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2732             true);
2733     if (!copyAnnotation)
2734     {
2735       /*
2736        * remove all groups and annotation except for the automatic stuff
2737        */
2738       newap.av.getAlignment().deleteAllGroups();
2739       newap.av.getAlignment().deleteAllAnnotations(false);
2740     }
2741
2742     newap.av.setGatherViewsHere(false);
2743
2744     if (viewport.viewName == null)
2745     {
2746       viewport.viewName = MessageManager
2747               .getString("label.view_name_original");
2748     }
2749
2750     /*
2751      * Views share the same edits undo and redo stacks
2752      */
2753     newap.av.setHistoryList(viewport.getHistoryList());
2754     newap.av.setRedoList(viewport.getRedoList());
2755
2756     /*
2757      * Views share the same mappings; need to deregister any new mappings
2758      * created by copyAlignPanel, and register the new reference to the shared
2759      * mappings
2760      */
2761     newap.av.replaceMappings(viewport.getAlignment());
2762
2763     newap.av.viewName = getNewViewName(viewTitle);
2764
2765     addAlignmentPanel(newap, true);
2766     newap.alignmentChanged();
2767
2768     if (alignPanels.size() == 2)
2769     {
2770       viewport.setGatherViewsHere(true);
2771     }
2772     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2773     return newap;
2774   }
2775
2776   /**
2777    * Make a new name for the view, ensuring it is unique within the current
2778    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2779    * these now use viewId. Unique view names are still desirable for usability.)
2780    *
2781    * @param viewTitle
2782    * @return
2783    */
2784   protected String getNewViewName(String viewTitle)
2785   {
2786     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2787     boolean addFirstIndex = false;
2788     if (viewTitle == null || viewTitle.trim().length() == 0)
2789     {
2790       viewTitle = MessageManager.getString("action.view");
2791       addFirstIndex = true;
2792     }
2793     else
2794     {
2795       index = 1;// we count from 1 if given a specific name
2796     }
2797     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2798
2799     List<Component> comps = PaintRefresher.components.get(viewport
2800             .getSequenceSetId());
2801
2802     List<String> existingNames = getExistingViewNames(comps);
2803
2804     while (existingNames.contains(newViewName))
2805     {
2806       newViewName = viewTitle + " " + (++index);
2807     }
2808     return newViewName;
2809   }
2810
2811   /**
2812    * Returns a list of distinct view names found in the given list of
2813    * components. View names are held on the viewport of an AlignmentPanel.
2814    *
2815    * @param comps
2816    * @return
2817    */
2818   protected List<String> getExistingViewNames(List<Component> comps)
2819   {
2820     List<String> existingNames = new ArrayList<String>();
2821     for (Component comp : comps)
2822     {
2823       if (comp instanceof AlignmentPanel)
2824       {
2825         AlignmentPanel ap = (AlignmentPanel) comp;
2826         if (!existingNames.contains(ap.av.viewName))
2827         {
2828           existingNames.add(ap.av.viewName);
2829         }
2830       }
2831     }
2832     return existingNames;
2833   }
2834
2835   /**
2836    * Explode tabbed views into separate windows.
2837    */
2838   @Override
2839   public void expandViews_actionPerformed(ActionEvent e)
2840   {
2841     Desktop.explodeViews(this);
2842   }
2843
2844   /**
2845    * Gather views in separate windows back into a tabbed presentation.
2846    */
2847   @Override
2848   public void gatherViews_actionPerformed(ActionEvent e)
2849   {
2850     Desktop.instance.gatherViews(this);
2851   }
2852
2853   /**
2854    * DOCUMENT ME!
2855    *
2856    * @param e
2857    *          DOCUMENT ME!
2858    */
2859   @Override
2860   public void font_actionPerformed(ActionEvent e)
2861   {
2862     new FontChooser(alignPanel);
2863   }
2864
2865   /**
2866    * DOCUMENT ME!
2867    *
2868    * @param e
2869    *          DOCUMENT ME!
2870    */
2871   @Override
2872   protected void seqLimit_actionPerformed(ActionEvent e)
2873   {
2874     viewport.setShowJVSuffix(seqLimits.isSelected());
2875
2876     alignPanel.getIdPanel().getIdCanvas()
2877             .setPreferredSize(alignPanel.calculateIdWidth());
2878     alignPanel.paintAlignment(true);
2879   }
2880
2881   @Override
2882   public void idRightAlign_actionPerformed(ActionEvent e)
2883   {
2884     viewport.setRightAlignIds(idRightAlign.isSelected());
2885     alignPanel.paintAlignment(true);
2886   }
2887
2888   @Override
2889   public void centreColumnLabels_actionPerformed(ActionEvent e)
2890   {
2891     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2892     alignPanel.paintAlignment(true);
2893   }
2894
2895   /*
2896    * (non-Javadoc)
2897    *
2898    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2899    */
2900   @Override
2901   protected void followHighlight_actionPerformed()
2902   {
2903     /*
2904      * Set the 'follow' flag on the Viewport (and scroll to position if now
2905      * true).
2906      */
2907     final boolean state = this.followHighlightMenuItem.getState();
2908     viewport.setFollowHighlight(state);
2909     if (state)
2910     {
2911       alignPanel.scrollToPosition(
2912               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2913     }
2914   }
2915
2916   /**
2917    * DOCUMENT ME!
2918    *
2919    * @param e
2920    *          DOCUMENT ME!
2921    */
2922   @Override
2923   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2924   {
2925     viewport.setColourText(colourTextMenuItem.isSelected());
2926     alignPanel.paintAlignment(true);
2927   }
2928
2929   /**
2930    * DOCUMENT ME!
2931    *
2932    * @param e
2933    *          DOCUMENT ME!
2934    */
2935   @Override
2936   public void wrapMenuItem_actionPerformed(ActionEvent e)
2937   {
2938     scaleAbove.setVisible(wrapMenuItem.isSelected());
2939     scaleLeft.setVisible(wrapMenuItem.isSelected());
2940     scaleRight.setVisible(wrapMenuItem.isSelected());
2941     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2942     alignPanel.updateLayout();
2943   }
2944
2945   @Override
2946   public void showAllSeqs_actionPerformed(ActionEvent e)
2947   {
2948     viewport.showAllHiddenSeqs();
2949   }
2950
2951   @Override
2952   public void showAllColumns_actionPerformed(ActionEvent e)
2953   {
2954     viewport.showAllHiddenColumns();
2955     repaint();
2956     viewport.sendSelection();
2957   }
2958
2959   @Override
2960   public void hideSelSequences_actionPerformed(ActionEvent e)
2961   {
2962     viewport.hideAllSelectedSeqs();
2963     // alignPanel.paintAlignment(true);
2964   }
2965
2966   /**
2967    * called by key handler and the hide all/show all menu items
2968    *
2969    * @param toggleSeqs
2970    * @param toggleCols
2971    */
2972   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2973   {
2974
2975     boolean hide = false;
2976     SequenceGroup sg = viewport.getSelectionGroup();
2977     if (!toggleSeqs && !toggleCols)
2978     {
2979       // Hide everything by the current selection - this is a hack - we do the
2980       // invert and then hide
2981       // first check that there will be visible columns after the invert.
2982       if (viewport.hasSelectedColumns()
2983               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2984                       .getEndRes()))
2985       {
2986         // now invert the sequence set, if required - empty selection implies
2987         // that no hiding is required.
2988         if (sg != null)
2989         {
2990           invertSequenceMenuItem_actionPerformed(null);
2991           sg = viewport.getSelectionGroup();
2992           toggleSeqs = true;
2993
2994         }
2995         viewport.expandColSelection(sg, true);
2996         // finally invert the column selection and get the new sequence
2997         // selection.
2998         invertColSel_actionPerformed(null);
2999         toggleCols = true;
3000       }
3001     }
3002
3003     if (toggleSeqs)
3004     {
3005       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3006       {
3007         hideSelSequences_actionPerformed(null);
3008         hide = true;
3009       }
3010       else if (!(toggleCols && viewport.hasSelectedColumns()))
3011       {
3012         showAllSeqs_actionPerformed(null);
3013       }
3014     }
3015
3016     if (toggleCols)
3017     {
3018       if (viewport.hasSelectedColumns())
3019       {
3020         hideSelColumns_actionPerformed(null);
3021         if (!toggleSeqs)
3022         {
3023           viewport.setSelectionGroup(sg);
3024         }
3025       }
3026       else if (!hide)
3027       {
3028         showAllColumns_actionPerformed(null);
3029       }
3030     }
3031   }
3032
3033   /*
3034    * (non-Javadoc)
3035    *
3036    * @see
3037    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3038    * event.ActionEvent)
3039    */
3040   @Override
3041   public void hideAllButSelection_actionPerformed(ActionEvent e)
3042   {
3043     toggleHiddenRegions(false, false);
3044     viewport.sendSelection();
3045   }
3046
3047   /*
3048    * (non-Javadoc)
3049    *
3050    * @see
3051    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3052    * .ActionEvent)
3053    */
3054   @Override
3055   public void hideAllSelection_actionPerformed(ActionEvent e)
3056   {
3057     SequenceGroup sg = viewport.getSelectionGroup();
3058     viewport.expandColSelection(sg, false);
3059     viewport.hideAllSelectedSeqs();
3060     viewport.hideSelectedColumns();
3061     alignPanel.paintAlignment(true);
3062     viewport.sendSelection();
3063   }
3064
3065   /*
3066    * (non-Javadoc)
3067    *
3068    * @see
3069    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3070    * ActionEvent)
3071    */
3072   @Override
3073   public void showAllhidden_actionPerformed(ActionEvent e)
3074   {
3075     viewport.showAllHiddenColumns();
3076     viewport.showAllHiddenSeqs();
3077     alignPanel.paintAlignment(true);
3078     viewport.sendSelection();
3079   }
3080
3081   @Override
3082   public void hideSelColumns_actionPerformed(ActionEvent e)
3083   {
3084     viewport.hideSelectedColumns();
3085     alignPanel.paintAlignment(true);
3086     viewport.sendSelection();
3087   }
3088
3089   @Override
3090   public void hiddenMarkers_actionPerformed(ActionEvent e)
3091   {
3092     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3093     repaint();
3094   }
3095
3096   /**
3097    * DOCUMENT ME!
3098    *
3099    * @param e
3100    *          DOCUMENT ME!
3101    */
3102   @Override
3103   protected void scaleAbove_actionPerformed(ActionEvent e)
3104   {
3105     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3106     alignPanel.paintAlignment(true);
3107   }
3108
3109   /**
3110    * DOCUMENT ME!
3111    *
3112    * @param e
3113    *          DOCUMENT ME!
3114    */
3115   @Override
3116   protected void scaleLeft_actionPerformed(ActionEvent e)
3117   {
3118     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3119     alignPanel.paintAlignment(true);
3120   }
3121
3122   /**
3123    * DOCUMENT ME!
3124    *
3125    * @param e
3126    *          DOCUMENT ME!
3127    */
3128   @Override
3129   protected void scaleRight_actionPerformed(ActionEvent e)
3130   {
3131     viewport.setScaleRightWrapped(scaleRight.isSelected());
3132     alignPanel.paintAlignment(true);
3133   }
3134
3135   /**
3136    * DOCUMENT ME!
3137    *
3138    * @param e
3139    *          DOCUMENT ME!
3140    */
3141   @Override
3142   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3143   {
3144     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3145     alignPanel.paintAlignment(true);
3146   }
3147
3148   /**
3149    * DOCUMENT ME!
3150    *
3151    * @param e
3152    *          DOCUMENT ME!
3153    */
3154   @Override
3155   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3156   {
3157     viewport.setShowText(viewTextMenuItem.isSelected());
3158     alignPanel.paintAlignment(true);
3159   }
3160
3161   /**
3162    * DOCUMENT ME!
3163    *
3164    * @param e
3165    *          DOCUMENT ME!
3166    */
3167   @Override
3168   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3169   {
3170     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3171     alignPanel.paintAlignment(true);
3172   }
3173
3174   public FeatureSettings featureSettings;
3175
3176   @Override
3177   public FeatureSettingsControllerI getFeatureSettingsUI()
3178   {
3179     return featureSettings;
3180   }
3181
3182   @Override
3183   public void featureSettings_actionPerformed(ActionEvent e)
3184   {
3185     if (featureSettings != null)
3186     {
3187       featureSettings.close();
3188       featureSettings = null;
3189     }
3190     if (!showSeqFeatures.isSelected())
3191     {
3192       // make sure features are actually displayed
3193       showSeqFeatures.setSelected(true);
3194       showSeqFeatures_actionPerformed(null);
3195     }
3196     featureSettings = new FeatureSettings(this);
3197   }
3198
3199   /**
3200    * Set or clear 'Show Sequence Features'
3201    *
3202    * @param evt
3203    *          DOCUMENT ME!
3204    */
3205   @Override
3206   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3207   {
3208     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3209     alignPanel.paintAlignment(true);
3210     if (alignPanel.getOverviewPanel() != null)
3211     {
3212       alignPanel.getOverviewPanel().updateOverviewImage();
3213     }
3214   }
3215
3216   /**
3217    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3218    * the annotations panel as a whole.
3219    *
3220    * The options to show/hide all annotations should be enabled when the panel
3221    * is shown, and disabled when the panel is hidden.
3222    *
3223    * @param e
3224    */
3225   @Override
3226   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3227   {
3228     final boolean setVisible = annotationPanelMenuItem.isSelected();
3229     viewport.setShowAnnotation(setVisible);
3230     this.showAllSeqAnnotations.setEnabled(setVisible);
3231     this.hideAllSeqAnnotations.setEnabled(setVisible);
3232     this.showAllAlAnnotations.setEnabled(setVisible);
3233     this.hideAllAlAnnotations.setEnabled(setVisible);
3234     alignPanel.updateLayout();
3235   }
3236
3237   @Override
3238   public void alignmentProperties()
3239   {
3240     JEditorPane editPane = new JEditorPane("text/html", "");
3241     editPane.setEditable(false);
3242     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3243             .formatAsHtml();
3244     editPane.setText(MessageManager.formatMessage("label.html_content",
3245             new Object[] { contents.toString() }));
3246     JInternalFrame frame = new JInternalFrame();
3247     frame.getContentPane().add(new JScrollPane(editPane));
3248
3249     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3250             "label.alignment_properties", new Object[] { getTitle() }),
3251             500, 400);
3252   }
3253
3254   /**
3255    * DOCUMENT ME!
3256    *
3257    * @param e
3258    *          DOCUMENT ME!
3259    */
3260   @Override
3261   public void overviewMenuItem_actionPerformed(ActionEvent e)
3262   {
3263     if (alignPanel.overviewPanel != null)
3264     {
3265       return;
3266     }
3267
3268     JInternalFrame frame = new JInternalFrame();
3269     OverviewPanel overview = new OverviewPanel(alignPanel);
3270     frame.setContentPane(overview);
3271     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3272             "label.overview_params", new Object[] { this.getTitle() }),
3273             frame.getWidth(), frame.getHeight());
3274     frame.pack();
3275     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3276     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3277     {
3278       @Override
3279       public void internalFrameClosed(
3280               javax.swing.event.InternalFrameEvent evt)
3281       {
3282         alignPanel.setOverviewPanel(null);
3283       };
3284     });
3285
3286     alignPanel.setOverviewPanel(overview);
3287   }
3288
3289   @Override
3290   public void textColour_actionPerformed(ActionEvent e)
3291   {
3292     new TextColourChooser().chooseColour(alignPanel, null);
3293   }
3294
3295   /**
3296    * DOCUMENT ME!
3297    *
3298    * @param e
3299    *          DOCUMENT ME!
3300    */
3301   @Override
3302   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3303   {
3304     changeColour(null);
3305   }
3306
3307   /**
3308    * DOCUMENT ME!
3309    *
3310    * @param e
3311    *          DOCUMENT ME!
3312    */
3313   @Override
3314   public void clustalColour_actionPerformed(ActionEvent e)
3315   {
3316     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3317             viewport.getHiddenRepSequences()));
3318   }
3319
3320   /**
3321    * DOCUMENT ME!
3322    *
3323    * @param e
3324    *          DOCUMENT ME!
3325    */
3326   @Override
3327   public void zappoColour_actionPerformed(ActionEvent e)
3328   {
3329     changeColour(new ZappoColourScheme());
3330   }
3331
3332   /**
3333    * DOCUMENT ME!
3334    *
3335    * @param e
3336    *          DOCUMENT ME!
3337    */
3338   @Override
3339   public void taylorColour_actionPerformed(ActionEvent e)
3340   {
3341     changeColour(new TaylorColourScheme());
3342   }
3343
3344   /**
3345    * DOCUMENT ME!
3346    *
3347    * @param e
3348    *          DOCUMENT ME!
3349    */
3350   @Override
3351   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3352   {
3353     changeColour(new HydrophobicColourScheme());
3354   }
3355
3356   /**
3357    * DOCUMENT ME!
3358    *
3359    * @param e
3360    *          DOCUMENT ME!
3361    */
3362   @Override
3363   public void helixColour_actionPerformed(ActionEvent e)
3364   {
3365     changeColour(new HelixColourScheme());
3366   }
3367
3368   /**
3369    * DOCUMENT ME!
3370    *
3371    * @param e
3372    *          DOCUMENT ME!
3373    */
3374   @Override
3375   public void strandColour_actionPerformed(ActionEvent e)
3376   {
3377     changeColour(new StrandColourScheme());
3378   }
3379
3380   /**
3381    * DOCUMENT ME!
3382    *
3383    * @param e
3384    *          DOCUMENT ME!
3385    */
3386   @Override
3387   public void turnColour_actionPerformed(ActionEvent e)
3388   {
3389     changeColour(new TurnColourScheme());
3390   }
3391
3392   /**
3393    * DOCUMENT ME!
3394    *
3395    * @param e
3396    *          DOCUMENT ME!
3397    */
3398   @Override
3399   public void buriedColour_actionPerformed(ActionEvent e)
3400   {
3401     changeColour(new BuriedColourScheme());
3402   }
3403
3404   /**
3405    * DOCUMENT ME!
3406    *
3407    * @param e
3408    *          DOCUMENT ME!
3409    */
3410   @Override
3411   public void nucleotideColour_actionPerformed(ActionEvent e)
3412   {
3413     changeColour(new NucleotideColourScheme());
3414   }
3415
3416   @Override
3417   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3418   {
3419     changeColour(new PurinePyrimidineColourScheme());
3420   }
3421
3422   /*
3423    * public void covariationColour_actionPerformed(ActionEvent e) {
3424    * changeColour(new
3425    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3426    * ()[0])); }
3427    */
3428   @Override
3429   public void annotationColour_actionPerformed(ActionEvent e)
3430   {
3431     new AnnotationColourChooser(viewport, alignPanel);
3432   }
3433
3434   @Override
3435   public void annotationColumn_actionPerformed(ActionEvent e)
3436   {
3437     new AnnotationColumnChooser(viewport, alignPanel);
3438   }
3439
3440   @Override
3441   public void rnahelicesColour_actionPerformed(ActionEvent e)
3442   {
3443     new RNAHelicesColourChooser(viewport, alignPanel);
3444   }
3445
3446   /**
3447    * DOCUMENT ME!
3448    *
3449    * @param e
3450    *          DOCUMENT ME!
3451    */
3452   @Override
3453   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3454   {
3455     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3456   }
3457
3458   /**
3459    * DOCUMENT ME!
3460    *
3461    * @param cs
3462    *          DOCUMENT ME!
3463    */
3464   @Override
3465   public void changeColour(ColourSchemeI cs)
3466   {
3467     // TODO: pull up to controller method
3468
3469     if (cs != null)
3470     {
3471       // Make sure viewport is up to date w.r.t. any sliders
3472       if (viewport.getAbovePIDThreshold())
3473       {
3474         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3475                 "Background");
3476         viewport.setThreshold(threshold);
3477       }
3478
3479       if (viewport.getConservationSelected())
3480       {
3481         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3482                 cs, "Background"));
3483       }
3484       if (cs instanceof TCoffeeColourScheme)
3485       {
3486         tcoffeeColour.setEnabled(true);
3487         tcoffeeColour.setSelected(true);
3488       }
3489     }
3490
3491     viewport.setGlobalColourScheme(cs);
3492
3493     alignPanel.paintAlignment(true);
3494   }
3495
3496   /**
3497    * DOCUMENT ME!
3498    *
3499    * @param e
3500    *          DOCUMENT ME!
3501    */
3502   @Override
3503   protected void modifyPID_actionPerformed(ActionEvent e)
3504   {
3505     if (viewport.getAbovePIDThreshold()
3506             && viewport.getGlobalColourScheme() != null)
3507     {
3508       SliderPanel.setPIDSliderSource(alignPanel,
3509               viewport.getGlobalColourScheme(), "Background");
3510       SliderPanel.showPIDSlider();
3511     }
3512   }
3513
3514   /**
3515    * DOCUMENT ME!
3516    *
3517    * @param e
3518    *          DOCUMENT ME!
3519    */
3520   @Override
3521   protected void modifyConservation_actionPerformed(ActionEvent e)
3522   {
3523     if (viewport.getConservationSelected()
3524             && viewport.getGlobalColourScheme() != null)
3525     {
3526       SliderPanel.setConservationSlider(alignPanel,
3527               viewport.getGlobalColourScheme(), "Background");
3528       SliderPanel.showConservationSlider();
3529     }
3530   }
3531
3532   /**
3533    * DOCUMENT ME!
3534    *
3535    * @param e
3536    *          DOCUMENT ME!
3537    */
3538   @Override
3539   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3540   {
3541     viewport.setConservationSelected(conservationMenuItem.isSelected());
3542
3543     viewport.setAbovePIDThreshold(false);
3544     abovePIDThreshold.setSelected(false);
3545
3546     changeColour(viewport.getGlobalColourScheme());
3547
3548     modifyConservation_actionPerformed(null);
3549   }
3550
3551   /**
3552    * DOCUMENT ME!
3553    *
3554    * @param e
3555    *          DOCUMENT ME!
3556    */
3557   @Override
3558   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3559   {
3560     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3561
3562     conservationMenuItem.setSelected(false);
3563     viewport.setConservationSelected(false);
3564
3565     changeColour(viewport.getGlobalColourScheme());
3566
3567     modifyPID_actionPerformed(null);
3568   }
3569
3570   /**
3571    * DOCUMENT ME!
3572    *
3573    * @param e
3574    *          DOCUMENT ME!
3575    */
3576   @Override
3577   public void userDefinedColour_actionPerformed(ActionEvent e)
3578   {
3579     if (e.getActionCommand().equals(
3580             MessageManager.getString("action.user_defined")))
3581     {
3582       new UserDefinedColours(alignPanel, null);
3583     }
3584     else
3585     {
3586       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3587               .getUserColourSchemes().get(e.getActionCommand());
3588
3589       changeColour(udc);
3590     }
3591   }
3592
3593   public void updateUserColourMenu()
3594   {
3595
3596     Component[] menuItems = colourMenu.getMenuComponents();
3597     int iSize = menuItems.length;
3598     for (int i = 0; i < iSize; i++)
3599     {
3600       if (menuItems[i].getName() != null
3601               && menuItems[i].getName().equals("USER_DEFINED"))
3602       {
3603         colourMenu.remove(menuItems[i]);
3604         iSize--;
3605       }
3606     }
3607     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3608     {
3609       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3610               .getUserColourSchemes().keys();
3611
3612       while (userColours.hasMoreElements())
3613       {
3614         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3615                 userColours.nextElement().toString());
3616         radioItem.setName("USER_DEFINED");
3617         radioItem.addMouseListener(new MouseAdapter()
3618         {
3619           @Override
3620           public void mousePressed(MouseEvent evt)
3621           {
3622             if (evt.isPopupTrigger()) // Mac
3623             {
3624               offerRemoval(radioItem);
3625             }
3626           }
3627
3628           @Override
3629           public void mouseReleased(MouseEvent evt)
3630           {
3631             if (evt.isPopupTrigger()) // Windows
3632             {
3633               offerRemoval(radioItem);
3634             }
3635           }
3636
3637           /**
3638            * @param radioItem
3639            */
3640           void offerRemoval(final JRadioButtonMenuItem radioItem)
3641           {
3642             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3643
3644             int option = JOptionPane.showInternalConfirmDialog(
3645                     jalview.gui.Desktop.desktop, MessageManager
3646                             .getString("label.remove_from_default_list"),
3647                     MessageManager
3648                             .getString("label.remove_user_defined_colour"),
3649                     JOptionPane.YES_NO_OPTION);
3650             if (option == JOptionPane.YES_OPTION)
3651             {
3652               jalview.gui.UserDefinedColours
3653                       .removeColourFromDefaults(radioItem.getText());
3654               colourMenu.remove(radioItem);
3655             }
3656             else
3657             {
3658               radioItem.addActionListener(new ActionListener()
3659               {
3660                 @Override
3661                 public void actionPerformed(ActionEvent evt)
3662                 {
3663                   userDefinedColour_actionPerformed(evt);
3664                 }
3665               });
3666             }
3667           }
3668         });
3669         radioItem.addActionListener(new ActionListener()
3670         {
3671           @Override
3672           public void actionPerformed(ActionEvent evt)
3673           {
3674             userDefinedColour_actionPerformed(evt);
3675           }
3676         });
3677
3678         colourMenu.insert(radioItem, 15);
3679         colours.add(radioItem);
3680       }
3681     }
3682   }
3683
3684   /**
3685    * DOCUMENT ME!
3686    *
3687    * @param e
3688    *          DOCUMENT ME!
3689    */
3690   @Override
3691   public void PIDColour_actionPerformed(ActionEvent e)
3692   {
3693     changeColour(new PIDColourScheme());
3694   }
3695
3696   /**
3697    * DOCUMENT ME!
3698    *
3699    * @param e
3700    *          DOCUMENT ME!
3701    */
3702   @Override
3703   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3704   {
3705     changeColour(new Blosum62ColourScheme());
3706   }
3707
3708   /**
3709    * DOCUMENT ME!
3710    *
3711    * @param e
3712    *          DOCUMENT ME!
3713    */
3714   @Override
3715   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3716   {
3717     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3718     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3719             .getAlignment().getSequenceAt(0), null);
3720     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3721             viewport.getAlignment()));
3722     alignPanel.paintAlignment(true);
3723   }
3724
3725   /**
3726    * DOCUMENT ME!
3727    *
3728    * @param e
3729    *          DOCUMENT ME!
3730    */
3731   @Override
3732   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3733   {
3734     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3735     AlignmentSorter.sortByID(viewport.getAlignment());
3736     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3737             viewport.getAlignment()));
3738     alignPanel.paintAlignment(true);
3739   }
3740
3741   /**
3742    * DOCUMENT ME!
3743    *
3744    * @param e
3745    *          DOCUMENT ME!
3746    */
3747   @Override
3748   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3749   {
3750     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751     AlignmentSorter.sortByLength(viewport.getAlignment());
3752     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3753             viewport.getAlignment()));
3754     alignPanel.paintAlignment(true);
3755   }
3756
3757   /**
3758    * DOCUMENT ME!
3759    *
3760    * @param e
3761    *          DOCUMENT ME!
3762    */
3763   @Override
3764   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3765   {
3766     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3767     AlignmentSorter.sortByGroup(viewport.getAlignment());
3768     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3769             viewport.getAlignment()));
3770
3771     alignPanel.paintAlignment(true);
3772   }
3773
3774   /**
3775    * DOCUMENT ME!
3776    *
3777    * @param e
3778    *          DOCUMENT ME!
3779    */
3780   @Override
3781   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3782   {
3783     new RedundancyPanel(alignPanel, this);
3784   }
3785
3786   /**
3787    * DOCUMENT ME!
3788    *
3789    * @param e
3790    *          DOCUMENT ME!
3791    */
3792   @Override
3793   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3794   {
3795     if ((viewport.getSelectionGroup() == null)
3796             || (viewport.getSelectionGroup().getSize() < 2))
3797     {
3798       JOptionPane.showInternalMessageDialog(this, MessageManager
3799               .getString("label.you_must_select_least_two_sequences"),
3800               MessageManager.getString("label.invalid_selection"),
3801               JOptionPane.WARNING_MESSAGE);
3802     }
3803     else
3804     {
3805       JInternalFrame frame = new JInternalFrame();
3806       frame.setContentPane(new PairwiseAlignPanel(viewport));
3807       Desktop.addInternalFrame(frame,
3808               MessageManager.getString("action.pairwise_alignment"), 600,
3809               500);
3810     }
3811   }
3812
3813   /**
3814    * DOCUMENT ME!
3815    *
3816    * @param e
3817    *          DOCUMENT ME!
3818    */
3819   @Override
3820   public void PCAMenuItem_actionPerformed(ActionEvent e)
3821   {
3822     if (((viewport.getSelectionGroup() != null)
3823             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3824             .getSelectionGroup().getSize() > 0))
3825             || (viewport.getAlignment().getHeight() < 4))
3826     {
3827       JOptionPane
3828               .showInternalMessageDialog(
3829                       this,
3830                       MessageManager
3831                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3832                       MessageManager
3833                               .getString("label.sequence_selection_insufficient"),
3834                       JOptionPane.WARNING_MESSAGE);
3835
3836       return;
3837     }
3838
3839     new PCAPanel(alignPanel);
3840   }
3841
3842   @Override
3843   public void autoCalculate_actionPerformed(ActionEvent e)
3844   {
3845     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3846     if (viewport.autoCalculateConsensus)
3847     {
3848       viewport.firePropertyChange("alignment", null, viewport
3849               .getAlignment().getSequences());
3850     }
3851   }
3852
3853   @Override
3854   public void sortByTreeOption_actionPerformed(ActionEvent e)
3855   {
3856     viewport.sortByTree = sortByTree.isSelected();
3857   }
3858
3859   @Override
3860   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3861   {
3862     viewport.followSelection = listenToViewSelections.isSelected();
3863   }
3864
3865   /**
3866    * DOCUMENT ME!
3867    *
3868    * @param e
3869    *          DOCUMENT ME!
3870    */
3871   @Override
3872   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3873   {
3874     newTreePanel("AV", "PID", "Average distance tree using PID");
3875   }
3876
3877   /**
3878    * DOCUMENT ME!
3879    *
3880    * @param e
3881    *          DOCUMENT ME!
3882    */
3883   @Override
3884   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3885   {
3886     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3887   }
3888
3889   /**
3890    * DOCUMENT ME!
3891    *
3892    * @param e
3893    *          DOCUMENT ME!
3894    */
3895   @Override
3896   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3897   {
3898     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3899   }
3900
3901   /**
3902    * DOCUMENT ME!
3903    *
3904    * @param e
3905    *          DOCUMENT ME!
3906    */
3907   @Override
3908   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3909   {
3910     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3911   }
3912
3913   /**
3914    * DOCUMENT ME!
3915    *
3916    * @param type
3917    *          DOCUMENT ME!
3918    * @param pwType
3919    *          DOCUMENT ME!
3920    * @param title
3921    *          DOCUMENT ME!
3922    */
3923   void newTreePanel(String type, String pwType, String title)
3924   {
3925     TreePanel tp;
3926
3927     if (viewport.getSelectionGroup() != null
3928             && viewport.getSelectionGroup().getSize() > 0)
3929     {
3930       if (viewport.getSelectionGroup().getSize() < 3)
3931       {
3932         JOptionPane
3933                 .showMessageDialog(
3934                         Desktop.desktop,
3935                         MessageManager
3936                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3937                         MessageManager
3938                                 .getString("label.not_enough_sequences"),
3939                         JOptionPane.WARNING_MESSAGE);
3940         return;
3941       }
3942
3943       SequenceGroup sg = viewport.getSelectionGroup();
3944
3945       /* Decide if the selection is a column region */
3946       for (SequenceI _s : sg.getSequences())
3947       {
3948         if (_s.getLength() < sg.getEndRes())
3949         {
3950           JOptionPane
3951                   .showMessageDialog(
3952                           Desktop.desktop,
3953                           MessageManager
3954                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3955                           MessageManager
3956                                   .getString("label.sequences_selection_not_aligned"),
3957                           JOptionPane.WARNING_MESSAGE);
3958
3959           return;
3960         }
3961       }
3962
3963       title = title + " on region";
3964       tp = new TreePanel(alignPanel, type, pwType);
3965     }
3966     else
3967     {
3968       // are the visible sequences aligned?
3969       if (!viewport.getAlignment().isAligned(false))
3970       {
3971         JOptionPane
3972                 .showMessageDialog(
3973                         Desktop.desktop,
3974                         MessageManager
3975                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3976                         MessageManager
3977                                 .getString("label.sequences_not_aligned"),
3978                         JOptionPane.WARNING_MESSAGE);
3979
3980         return;
3981       }
3982
3983       if (viewport.getAlignment().getHeight() < 2)
3984       {
3985         return;
3986       }
3987
3988       tp = new TreePanel(alignPanel, type, pwType);
3989     }
3990
3991     title += " from ";
3992
3993     if (viewport.viewName != null)
3994     {
3995       title += viewport.viewName + " of ";
3996     }
3997
3998     title += this.title;
3999
4000     Desktop.addInternalFrame(tp, title, 600, 500);
4001   }
4002
4003   /**
4004    * DOCUMENT ME!
4005    *
4006    * @param title
4007    *          DOCUMENT ME!
4008    * @param order
4009    *          DOCUMENT ME!
4010    */
4011   public void addSortByOrderMenuItem(String title,
4012           final AlignmentOrder order)
4013   {
4014     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4015             "action.by_title_param", new Object[] { title }));
4016     sort.add(item);
4017     item.addActionListener(new java.awt.event.ActionListener()
4018     {
4019       @Override
4020       public void actionPerformed(ActionEvent e)
4021       {
4022         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4023
4024         // TODO: JBPNote - have to map order entries to curent SequenceI
4025         // pointers
4026         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4027
4028         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4029                 .getAlignment()));
4030
4031         alignPanel.paintAlignment(true);
4032       }
4033     });
4034   }
4035
4036   /**
4037    * Add a new sort by annotation score menu item
4038    *
4039    * @param sort
4040    *          the menu to add the option to
4041    * @param scoreLabel
4042    *          the label used to retrieve scores for each sequence on the
4043    *          alignment
4044    */
4045   public void addSortByAnnotScoreMenuItem(JMenu sort,
4046           final String scoreLabel)
4047   {
4048     final JMenuItem item = new JMenuItem(scoreLabel);
4049     sort.add(item);
4050     item.addActionListener(new java.awt.event.ActionListener()
4051     {
4052       @Override
4053       public void actionPerformed(ActionEvent e)
4054       {
4055         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4056         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4057                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4058         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4059                 viewport.getAlignment()));
4060         alignPanel.paintAlignment(true);
4061       }
4062     });
4063   }
4064
4065   /**
4066    * last hash for alignment's annotation array - used to minimise cost of
4067    * rebuild.
4068    */
4069   protected int _annotationScoreVectorHash;
4070
4071   /**
4072    * search the alignment and rebuild the sort by annotation score submenu the
4073    * last alignment annotation vector hash is stored to minimize cost of
4074    * rebuilding in subsequence calls.
4075    *
4076    */
4077   @Override
4078   public void buildSortByAnnotationScoresMenu()
4079   {
4080     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4081     {
4082       return;
4083     }
4084
4085     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4086     {
4087       sortByAnnotScore.removeAll();
4088       // almost certainly a quicker way to do this - but we keep it simple
4089       Hashtable scoreSorts = new Hashtable();
4090       AlignmentAnnotation aann[];
4091       for (SequenceI sqa : viewport.getAlignment().getSequences())
4092       {
4093         aann = sqa.getAnnotation();
4094         for (int i = 0; aann != null && i < aann.length; i++)
4095         {
4096           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4097           {
4098             scoreSorts.put(aann[i].label, aann[i].label);
4099           }
4100         }
4101       }
4102       Enumeration labels = scoreSorts.keys();
4103       while (labels.hasMoreElements())
4104       {
4105         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4106                 (String) labels.nextElement());
4107       }
4108       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4109       scoreSorts.clear();
4110
4111       _annotationScoreVectorHash = viewport.getAlignment()
4112               .getAlignmentAnnotation().hashCode();
4113     }
4114   }
4115
4116   /**
4117    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4118    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4119    * call. Listeners are added to remove the menu item when the treePanel is
4120    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4121    * modified.
4122    *
4123    * @param treePanel
4124    *          Displayed tree window.
4125    * @param title
4126    *          SortBy menu item title.
4127    */
4128   @Override
4129   public void buildTreeMenu()
4130   {
4131     calculateTree.removeAll();
4132     // build the calculate menu
4133
4134     for (final String type : new String[] { "NJ", "AV" })
4135     {
4136       String treecalcnm = MessageManager.getString("label.tree_calc_"
4137               + type.toLowerCase());
4138       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4139       {
4140         JMenuItem tm = new JMenuItem();
4141         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4142         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4143                 || sm.isProtein() == !viewport.getAlignment()
4144                         .isNucleotide())
4145         {
4146           String smn = MessageManager.getStringOrReturn(
4147                   "label.score_model_", sm.getName());
4148           final String title = MessageManager.formatMessage(
4149                   "label.treecalc_title", treecalcnm, smn);
4150           tm.setText(title);//
4151           tm.addActionListener(new java.awt.event.ActionListener()
4152           {
4153             @Override
4154             public void actionPerformed(ActionEvent e)
4155             {
4156               newTreePanel(type, pwtype, title);
4157             }
4158           });
4159           calculateTree.add(tm);
4160         }
4161
4162       }
4163     }
4164     sortByTreeMenu.removeAll();
4165
4166     List<Component> comps = PaintRefresher.components.get(viewport
4167             .getSequenceSetId());
4168     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4169     for (Component comp : comps)
4170     {
4171       if (comp instanceof TreePanel)
4172       {
4173         treePanels.add((TreePanel) comp);
4174       }
4175     }
4176
4177     if (treePanels.size() < 1)
4178     {
4179       sortByTreeMenu.setVisible(false);
4180       return;
4181     }
4182
4183     sortByTreeMenu.setVisible(true);
4184
4185     for (final TreePanel tp : treePanels)
4186     {
4187       final JMenuItem item = new JMenuItem(tp.getTitle());
4188       item.addActionListener(new java.awt.event.ActionListener()
4189       {
4190         @Override
4191         public void actionPerformed(ActionEvent e)
4192         {
4193           tp.sortByTree_actionPerformed();
4194           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4195
4196         }
4197       });
4198
4199       sortByTreeMenu.add(item);
4200     }
4201   }
4202
4203   public boolean sortBy(AlignmentOrder alorder, String undoname)
4204   {
4205     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4206     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4207     if (undoname != null)
4208     {
4209       addHistoryItem(new OrderCommand(undoname, oldOrder,
4210               viewport.getAlignment()));
4211     }
4212     alignPanel.paintAlignment(true);
4213     return true;
4214   }
4215
4216   /**
4217    * Work out whether the whole set of sequences or just the selected set will
4218    * be submitted for multiple alignment.
4219    *
4220    */
4221   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4222   {
4223     // Now, check we have enough sequences
4224     AlignmentView msa = null;
4225
4226     if ((viewport.getSelectionGroup() != null)
4227             && (viewport.getSelectionGroup().getSize() > 1))
4228     {
4229       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4230       // some common interface!
4231       /*
4232        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4233        * SequenceI[sz = seqs.getSize(false)];
4234        *
4235        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4236        * seqs.getSequenceAt(i); }
4237        */
4238       msa = viewport.getAlignmentView(true);
4239     }
4240     else if (viewport.getSelectionGroup() != null
4241             && viewport.getSelectionGroup().getSize() == 1)
4242     {
4243       int option = JOptionPane.showConfirmDialog(this,
4244               MessageManager.getString("warn.oneseq_msainput_selection"),
4245               MessageManager.getString("label.invalid_selection"),
4246               JOptionPane.OK_CANCEL_OPTION);
4247       if (option == JOptionPane.OK_OPTION)
4248       {
4249         msa = viewport.getAlignmentView(false);
4250       }
4251     }
4252     else
4253     {
4254       msa = viewport.getAlignmentView(false);
4255     }
4256     return msa;
4257   }
4258
4259   /**
4260    * Decides what is submitted to a secondary structure prediction service: the
4261    * first sequence in the alignment, or in the current selection, or, if the
4262    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4263    * region or the whole alignment. (where the first sequence in the set is the
4264    * one that the prediction will be for).
4265    */
4266   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4267   {
4268     AlignmentView seqs = null;
4269
4270     if ((viewport.getSelectionGroup() != null)
4271             && (viewport.getSelectionGroup().getSize() > 0))
4272     {
4273       seqs = viewport.getAlignmentView(true);
4274     }
4275     else
4276     {
4277       seqs = viewport.getAlignmentView(false);
4278     }
4279     // limit sequences - JBPNote in future - could spawn multiple prediction
4280     // jobs
4281     // TODO: viewport.getAlignment().isAligned is a global state - the local
4282     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4283     if (!viewport.getAlignment().isAligned(false))
4284     {
4285       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4286       // TODO: if seqs.getSequences().length>1 then should really have warned
4287       // user!
4288
4289     }
4290     return seqs;
4291   }
4292
4293   /**
4294    * DOCUMENT ME!
4295    *
4296    * @param e
4297    *          DOCUMENT ME!
4298    */
4299   @Override
4300   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4301   {
4302     // Pick the tree file
4303     JalviewFileChooser chooser = new JalviewFileChooser(
4304             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4305     chooser.setFileView(new JalviewFileView());
4306     chooser.setDialogTitle(MessageManager
4307             .getString("label.select_newick_like_tree_file"));
4308     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4309
4310     int value = chooser.showOpenDialog(null);
4311
4312     if (value == JalviewFileChooser.APPROVE_OPTION)
4313     {
4314       String choice = chooser.getSelectedFile().getPath();
4315       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4316       jalview.io.NewickFile fin = null;
4317       try
4318       {
4319         fin = new jalview.io.NewickFile(choice, "File");
4320         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4321       } catch (Exception ex)
4322       {
4323         JOptionPane
4324                 .showMessageDialog(
4325                         Desktop.desktop,
4326                         ex.getMessage(),
4327                         MessageManager
4328                                 .getString("label.problem_reading_tree_file"),
4329                         JOptionPane.WARNING_MESSAGE);
4330         ex.printStackTrace();
4331       }
4332       if (fin != null && fin.hasWarningMessage())
4333       {
4334         JOptionPane.showMessageDialog(Desktop.desktop, fin
4335                 .getWarningMessage(), MessageManager
4336                 .getString("label.possible_problem_with_tree_file"),
4337                 JOptionPane.WARNING_MESSAGE);
4338       }
4339     }
4340   }
4341
4342   @Override
4343   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4344   {
4345     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4346   }
4347
4348   public TreePanel ShowNewickTree(NewickFile nf, String title)
4349   {
4350     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4351   }
4352
4353   public TreePanel ShowNewickTree(NewickFile nf, String title,
4354           AlignmentView input)
4355   {
4356     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4357   }
4358
4359   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4360           int h, int x, int y)
4361   {
4362     return ShowNewickTree(nf, title, null, w, h, x, y);
4363   }
4364
4365   /**
4366    * Add a treeviewer for the tree extracted from a newick file object to the
4367    * current alignment view
4368    *
4369    * @param nf
4370    *          the tree
4371    * @param title
4372    *          tree viewer title
4373    * @param input
4374    *          Associated alignment input data (or null)
4375    * @param w
4376    *          width
4377    * @param h
4378    *          height
4379    * @param x
4380    *          position
4381    * @param y
4382    *          position
4383    * @return TreePanel handle
4384    */
4385   public TreePanel ShowNewickTree(NewickFile nf, String title,
4386           AlignmentView input, int w, int h, int x, int y)
4387   {
4388     TreePanel tp = null;
4389
4390     try
4391     {
4392       nf.parse();
4393
4394       if (nf.getTree() != null)
4395       {
4396         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4397
4398         tp.setSize(w, h);
4399
4400         if (x > 0 && y > 0)
4401         {
4402           tp.setLocation(x, y);
4403         }
4404
4405         Desktop.addInternalFrame(tp, title, w, h);
4406       }
4407     } catch (Exception ex)
4408     {
4409       ex.printStackTrace();
4410     }
4411
4412     return tp;
4413   }
4414
4415   private boolean buildingMenu = false;
4416
4417   /**
4418    * Generates menu items and listener event actions for web service clients
4419    *
4420    */
4421   public void BuildWebServiceMenu()
4422   {
4423     while (buildingMenu)
4424     {
4425       try
4426       {
4427         System.err.println("Waiting for building menu to finish.");
4428         Thread.sleep(10);
4429       } catch (Exception e)
4430       {
4431       }
4432     }
4433     final AlignFrame me = this;
4434     buildingMenu = true;
4435     new Thread(new Runnable()
4436     {
4437       @Override
4438       public void run()
4439       {
4440         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4441         try
4442         {
4443           // System.err.println("Building ws menu again "
4444           // + Thread.currentThread());
4445           // TODO: add support for context dependent disabling of services based
4446           // on
4447           // alignment and current selection
4448           // TODO: add additional serviceHandle parameter to specify abstract
4449           // handler
4450           // class independently of AbstractName
4451           // TODO: add in rediscovery GUI function to restart discoverer
4452           // TODO: group services by location as well as function and/or
4453           // introduce
4454           // object broker mechanism.
4455           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4456           final IProgressIndicator af = me;
4457
4458           /*
4459            * do not i18n these strings - they are hard-coded in class
4460            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4461            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4462            */
4463           final JMenu msawsmenu = new JMenu("Alignment");
4464           final JMenu secstrmenu = new JMenu(
4465                   "Secondary Structure Prediction");
4466           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4467           final JMenu analymenu = new JMenu("Analysis");
4468           final JMenu dismenu = new JMenu("Protein Disorder");
4469           // JAL-940 - only show secondary structure prediction services from
4470           // the legacy server
4471           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4472               // &&
4473           Discoverer.services != null && (Discoverer.services.size() > 0))
4474           {
4475             // TODO: refactor to allow list of AbstractName/Handler bindings to
4476             // be
4477             // stored or retrieved from elsewhere
4478             // No MSAWS used any more:
4479             // Vector msaws = null; // (Vector)
4480             // Discoverer.services.get("MsaWS");
4481             Vector secstrpr = (Vector) Discoverer.services
4482                     .get("SecStrPred");
4483             if (secstrpr != null)
4484             {
4485               // Add any secondary structure prediction services
4486               for (int i = 0, j = secstrpr.size(); i < j; i++)
4487               {
4488                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4489                         .get(i);
4490                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4491                         .getServiceClient(sh);
4492                 int p = secstrmenu.getItemCount();
4493                 impl.attachWSMenuEntry(secstrmenu, me);
4494                 int q = secstrmenu.getItemCount();
4495                 for (int litm = p; litm < q; litm++)
4496                 {
4497                   legacyItems.add(secstrmenu.getItem(litm));
4498                 }
4499               }
4500             }
4501           }
4502
4503           // Add all submenus in the order they should appear on the web
4504           // services menu
4505           wsmenu.add(msawsmenu);
4506           wsmenu.add(secstrmenu);
4507           wsmenu.add(dismenu);
4508           wsmenu.add(analymenu);
4509           // No search services yet
4510           // wsmenu.add(seqsrchmenu);
4511
4512           javax.swing.SwingUtilities.invokeLater(new Runnable()
4513           {
4514             @Override
4515             public void run()
4516             {
4517               try
4518               {
4519                 webService.removeAll();
4520                 // first, add discovered services onto the webservices menu
4521                 if (wsmenu.size() > 0)
4522                 {
4523                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4524                   {
4525                     webService.add(wsmenu.get(i));
4526                   }
4527                 }
4528                 else
4529                 {
4530                   webService.add(me.webServiceNoServices);
4531                 }
4532                 // TODO: move into separate menu builder class.
4533                 boolean new_sspred = false;
4534                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4535                 {
4536                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4537                   if (jws2servs != null)
4538                   {
4539                     if (jws2servs.hasServices())
4540                     {
4541                       jws2servs.attachWSMenuEntry(webService, me);
4542                       for (Jws2Instance sv : jws2servs.getServices())
4543                       {
4544                         if (sv.description.toLowerCase().contains("jpred"))
4545                         {
4546                           for (JMenuItem jmi : legacyItems)
4547                           {
4548                             jmi.setVisible(false);
4549                           }
4550                         }
4551                       }
4552
4553                     }
4554                     if (jws2servs.isRunning())
4555                     {
4556                       JMenuItem tm = new JMenuItem(
4557                               "Still discovering JABA Services");
4558                       tm.setEnabled(false);
4559                       webService.add(tm);
4560                     }
4561                   }
4562                 }
4563                 build_urlServiceMenu(me.webService);
4564                 build_fetchdbmenu(webService);
4565                 for (JMenu item : wsmenu)
4566                 {
4567                   if (item.getItemCount() == 0)
4568                   {
4569                     item.setEnabled(false);
4570                   }
4571                   else
4572                   {
4573                     item.setEnabled(true);
4574                   }
4575                 }
4576               } catch (Exception e)
4577               {
4578                 Cache.log
4579                         .debug("Exception during web service menu building process.",
4580                                 e);
4581               }
4582             }
4583           });
4584         } catch (Exception e)
4585         {
4586         }
4587         buildingMenu = false;
4588       }
4589     }).start();
4590
4591   }
4592
4593   /**
4594    * construct any groupURL type service menu entries.
4595    *
4596    * @param webService
4597    */
4598   private void build_urlServiceMenu(JMenu webService)
4599   {
4600     // TODO: remove this code when 2.7 is released
4601     // DEBUG - alignmentView
4602     /*
4603      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4604      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4605      *
4606      * @Override public void actionPerformed(ActionEvent e) {
4607      * jalview.datamodel.AlignmentView
4608      * .testSelectionViews(af.viewport.getAlignment(),
4609      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4610      *
4611      * }); webService.add(testAlView);
4612      */
4613     // TODO: refactor to RestClient discoverer and merge menu entries for
4614     // rest-style services with other types of analysis/calculation service
4615     // SHmmr test client - still being implemented.
4616     // DEBUG - alignmentView
4617
4618     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4619             .getRestClients())
4620     {
4621       client.attachWSMenuEntry(
4622               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4623               this);
4624     }
4625   }
4626
4627   /**
4628    * Searches the alignment sequences for xRefs and builds the Show
4629    * Cross-References menu (formerly called Show Products), with database
4630    * sources for which cross-references are found (protein sources for a
4631    * nucleotide alignment and vice versa)
4632    *
4633    * @return true if Show Cross-references menu should be enabled
4634    */
4635   public boolean canShowProducts()
4636   {
4637     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4638     AlignmentI dataset = viewport.getAlignment().getDataset();
4639
4640     showProducts.removeAll();
4641     final boolean dna = viewport.getAlignment().isNucleotide();
4642
4643     if (seqs == null || seqs.length == 0)
4644     {
4645       // nothing to see here.
4646       return false;
4647     }
4648
4649     boolean showp = false;
4650     try
4651     {
4652       List<String> ptypes = new CrossRef(seqs, dataset)
4653               .findXrefSourcesForSequences(dna);
4654
4655       for (final String source : ptypes)
4656       {
4657         showp = true;
4658         final AlignFrame af = this;
4659         JMenuItem xtype = new JMenuItem(source);
4660         xtype.addActionListener(new ActionListener()
4661         {
4662           @Override
4663           public void actionPerformed(ActionEvent e)
4664           {
4665             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4666           }
4667         });
4668         showProducts.add(xtype);
4669       }
4670       showProducts.setVisible(showp);
4671       showProducts.setEnabled(showp);
4672     } catch (Exception e)
4673     {
4674       Cache.log
4675               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4676                       e);
4677       return false;
4678     }
4679     return showp;
4680   }
4681
4682   /**
4683    * Finds and displays cross-references for the selected sequences (protein
4684    * products for nucleotide sequences, dna coding sequences for peptides).
4685    *
4686    * @param sel
4687    *          the sequences to show cross-references for
4688    * @param dna
4689    *          true if from a nucleotide alignment (so showing proteins)
4690    * @param source
4691    *          the database to show cross-references for
4692    */
4693   protected void showProductsFor(final SequenceI[] sel,
4694           final boolean _odna, final String source)
4695   {
4696     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4697             .start();
4698   }
4699
4700   /**
4701    * Construct and display a new frame containing the translation of this
4702    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4703    */
4704   @Override
4705   public void showTranslation_actionPerformed(ActionEvent e)
4706   {
4707     AlignmentI al = null;
4708     try
4709     {
4710       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4711
4712       al = dna.translateCdna();
4713     } catch (Exception ex)
4714     {
4715       jalview.bin.Cache.log.error(
4716               "Exception during translation. Please report this !", ex);
4717       final String msg = MessageManager
4718               .getString("label.error_when_translating_sequences_submit_bug_report");
4719       final String errorTitle = MessageManager
4720               .getString("label.implementation_error")
4721               + MessageManager.getString("label.translation_failed");
4722       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4723               JOptionPane.ERROR_MESSAGE);
4724       return;
4725     }
4726     if (al == null || al.getHeight() == 0)
4727     {
4728       final String msg = MessageManager
4729               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4730       final String errorTitle = MessageManager
4731               .getString("label.translation_failed");
4732       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4733               JOptionPane.WARNING_MESSAGE);
4734     }
4735     else
4736     {
4737       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4738       af.setFileFormat(this.currentFileFormat);
4739       final String newTitle = MessageManager.formatMessage(
4740               "label.translation_of_params",
4741               new Object[] { this.getTitle() });
4742       af.setTitle(newTitle);
4743       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4744       {
4745         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4746         viewport.openSplitFrame(af, new Alignment(seqs));
4747       }
4748       else
4749       {
4750         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4751                 DEFAULT_HEIGHT);
4752       }
4753     }
4754   }
4755
4756   /**
4757    * Set the file format
4758    *
4759    * @param fileFormat
4760    */
4761   public void setFileFormat(String fileFormat)
4762   {
4763     this.currentFileFormat = fileFormat;
4764   }
4765
4766   /**
4767    * Try to load a features file onto the alignment.
4768    *
4769    * @param file
4770    *          contents or path to retrieve file
4771    * @param type
4772    *          access mode of file (see jalview.io.AlignFile)
4773    * @return true if features file was parsed correctly.
4774    */
4775   public boolean parseFeaturesFile(String file, String type)
4776   {
4777     return avc.parseFeaturesFile(file, type,
4778             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4779
4780   }
4781
4782   @Override
4783   public void refreshFeatureUI(boolean enableIfNecessary)
4784   {
4785     // note - currently this is only still here rather than in the controller
4786     // because of the featureSettings hard reference that is yet to be
4787     // abstracted
4788     if (enableIfNecessary)
4789     {
4790       viewport.setShowSequenceFeatures(true);
4791       showSeqFeatures.setSelected(true);
4792     }
4793
4794   }
4795
4796   @Override
4797   public void dragEnter(DropTargetDragEvent evt)
4798   {
4799   }
4800
4801   @Override
4802   public void dragExit(DropTargetEvent evt)
4803   {
4804   }
4805
4806   @Override
4807   public void dragOver(DropTargetDragEvent evt)
4808   {
4809   }
4810
4811   @Override
4812   public void dropActionChanged(DropTargetDragEvent evt)
4813   {
4814   }
4815
4816   @Override
4817   public void drop(DropTargetDropEvent evt)
4818   {
4819     // JAL-1552 - acceptDrop required before getTransferable call for
4820     // Java's Transferable for native dnd
4821     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4822     Transferable t = evt.getTransferable();
4823     java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
4824
4825     try
4826     {
4827       Desktop.transferFromDropTarget(files, protocols, evt, t);
4828     } catch (Exception e)
4829     {
4830       e.printStackTrace();
4831     }
4832     if (files != null)
4833     {
4834       try
4835       {
4836         // check to see if any of these files have names matching sequences in
4837         // the alignment
4838         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4839                 .getAlignment().getSequencesArray());
4840         /**
4841          * Object[] { String,SequenceI}
4842          */
4843         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4844         ArrayList<String> filesnotmatched = new ArrayList<String>();
4845         for (int i = 0; i < files.size(); i++)
4846         {
4847           String file = files.get(i).toString();
4848           String pdbfn = "";
4849           String protocol = FormatAdapter.checkProtocol(file);
4850           if (protocol == jalview.io.FormatAdapter.FILE)
4851           {
4852             File fl = new File(file);
4853             pdbfn = fl.getName();
4854           }
4855           else if (protocol == jalview.io.FormatAdapter.URL)
4856           {
4857             URL url = new URL(file);
4858             pdbfn = url.getFile();
4859           }
4860           if (pdbfn.length() > 0)
4861           {
4862             // attempt to find a match in the alignment
4863             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4864             int l = 0, c = pdbfn.indexOf(".");
4865             while (mtch == null && c != -1)
4866             {
4867               do
4868               {
4869                 l = c;
4870               } while ((c = pdbfn.indexOf(".", l)) > l);
4871               if (l > -1)
4872               {
4873                 pdbfn = pdbfn.substring(0, l);
4874               }
4875               mtch = idm.findAllIdMatches(pdbfn);
4876             }
4877             if (mtch != null)
4878             {
4879               String type = null;
4880               try
4881               {
4882                 type = new IdentifyFile().identify(file, protocol);
4883               } catch (Exception ex)
4884               {
4885                 type = null;
4886               }
4887               if (type != null)
4888               {
4889                 if (StructureFile.isStructureFile(type))
4890                 {
4891                   filesmatched.add(new Object[] { file, protocol, mtch });
4892                   continue;
4893                 }
4894               }
4895             }
4896             // File wasn't named like one of the sequences or wasn't a PDB file.
4897             filesnotmatched.add(file);
4898           }
4899         }
4900         int assocfiles = 0;
4901         if (filesmatched.size() > 0)
4902         {
4903           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4904                   || JOptionPane
4905                           .showConfirmDialog(
4906                                   this,
4907                                   MessageManager
4908                                           .formatMessage(
4909                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4910                                                   new Object[] { Integer
4911                                                           .valueOf(
4912                                                                   filesmatched
4913                                                                           .size())
4914                                                           .toString() }),
4915                                   MessageManager
4916                                           .getString("label.automatically_associate_structure_files_by_name"),
4917                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4918
4919           {
4920             for (Object[] fm : filesmatched)
4921             {
4922               // try and associate
4923               // TODO: may want to set a standard ID naming formalism for
4924               // associating PDB files which have no IDs.
4925               for (SequenceI toassoc : (SequenceI[]) fm[2])
4926               {
4927                 PDBEntry pe = new AssociatePdbFileWithSeq()
4928                         .associatePdbWithSeq((String) fm[0],
4929                                 (String) fm[1], toassoc, false,
4930                                 Desktop.instance);
4931                 if (pe != null)
4932                 {
4933                   System.err.println("Associated file : "
4934                           + ((String) fm[0]) + " with "
4935                           + toassoc.getDisplayId(true));
4936                   assocfiles++;
4937                 }
4938               }
4939               alignPanel.paintAlignment(true);
4940             }
4941           }
4942         }
4943         if (filesnotmatched.size() > 0)
4944         {
4945           if (assocfiles > 0
4946                   && (Cache.getDefault(
4947                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4948                           .showConfirmDialog(
4949                                   this,
4950                                   "<html>"
4951                                           + MessageManager
4952                                                   .formatMessage(
4953                                                           "label.ignore_unmatched_dropped_files_info",
4954                                                           new Object[] { Integer
4955                                                                   .valueOf(
4956                                                                           filesnotmatched
4957                                                                                   .size())
4958                                                                   .toString() })
4959                                           + "</html>",
4960                                   MessageManager
4961                                           .getString("label.ignore_unmatched_dropped_files"),
4962                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4963           {
4964             return;
4965           }
4966           for (String fn : filesnotmatched)
4967           {
4968             loadJalviewDataFile(fn, null, null, null);
4969           }
4970
4971         }
4972       } catch (Exception ex)
4973       {
4974         ex.printStackTrace();
4975       }
4976     }
4977   }
4978
4979   /**
4980    * Attempt to load a "dropped" file or URL string: First by testing whether
4981    * it's an Annotation file, then a JNet file, and finally a features file. If
4982    * all are false then the user may have dropped an alignment file onto this
4983    * AlignFrame.
4984    *
4985    * @param file
4986    *          either a filename or a URL string.
4987    */
4988   public void loadJalviewDataFile(String file, String protocol,
4989           String format, SequenceI assocSeq)
4990   {
4991     try
4992     {
4993       if (protocol == null)
4994       {
4995         protocol = FormatAdapter.checkProtocol(file);
4996       }
4997       // if the file isn't identified, or not positively identified as some
4998       // other filetype (PFAM is default unidentified alignment file type) then
4999       // try to parse as annotation.
5000       boolean isAnnotation = (format == null || format
5001               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5002               .annotateAlignmentView(viewport, file, protocol) : false;
5003
5004       if (!isAnnotation)
5005       {
5006         // first see if its a T-COFFEE score file
5007         TCoffeeScoreFile tcf = null;
5008         try
5009         {
5010           tcf = new TCoffeeScoreFile(file, protocol);
5011           if (tcf.isValid())
5012           {
5013             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5014             {
5015               tcoffeeColour.setEnabled(true);
5016               tcoffeeColour.setSelected(true);
5017               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5018               isAnnotation = true;
5019               statusBar
5020                       .setText(MessageManager
5021                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5022             }
5023             else
5024             {
5025               // some problem - if no warning its probable that the ID matching
5026               // process didn't work
5027               JOptionPane
5028                       .showMessageDialog(
5029                               Desktop.desktop,
5030                               tcf.getWarningMessage() == null ? MessageManager
5031                                       .getString("label.check_file_matches_sequence_ids_alignment")
5032                                       : tcf.getWarningMessage(),
5033                               MessageManager
5034                                       .getString("label.problem_reading_tcoffee_score_file"),
5035                               JOptionPane.WARNING_MESSAGE);
5036             }
5037           }
5038           else
5039           {
5040             tcf = null;
5041           }
5042         } catch (Exception x)
5043         {
5044           Cache.log
5045                   .debug("Exception when processing data source as T-COFFEE score file",
5046                           x);
5047           tcf = null;
5048         }
5049         if (tcf == null)
5050         {
5051           // try to see if its a JNet 'concise' style annotation file *before*
5052           // we
5053           // try to parse it as a features file
5054           if (format == null)
5055           {
5056             format = new IdentifyFile().identify(file, protocol);
5057           }
5058           if (format.equalsIgnoreCase("JnetFile"))
5059           {
5060             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5061                     file, protocol);
5062             new JnetAnnotationMaker();
5063             JnetAnnotationMaker.add_annotation(predictions,
5064                     viewport.getAlignment(), 0, false);
5065             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5066             viewport.getAlignment().setSeqrep(repseq);
5067             ColumnSelection cs = new ColumnSelection();
5068             cs.hideInsertionsFor(repseq);
5069             viewport.setColumnSelection(cs);
5070             isAnnotation = true;
5071           }
5072           else if (IdentifyFile.FeaturesFile.equals(format))
5073           {
5074             if (parseFeaturesFile(file, protocol))
5075             {
5076               alignPanel.paintAlignment(true);
5077             }
5078           }
5079           else
5080           {
5081             new FileLoader().LoadFile(viewport, file, protocol, format);
5082           }
5083         }
5084       }
5085       if (isAnnotation)
5086       {
5087
5088         alignPanel.adjustAnnotationHeight();
5089         viewport.updateSequenceIdColours();
5090         buildSortByAnnotationScoresMenu();
5091         alignPanel.paintAlignment(true);
5092       }
5093     } catch (Exception ex)
5094     {
5095       ex.printStackTrace();
5096     } catch (OutOfMemoryError oom)
5097     {
5098       try
5099       {
5100         System.gc();
5101       } catch (Exception x)
5102       {
5103       }
5104       new OOMWarning(
5105               "loading data "
5106                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5107                               : "using " + protocol + " from " + file)
5108                               : ".")
5109                       + (format != null ? "(parsing as '" + format
5110                               + "' file)" : ""), oom, Desktop.desktop);
5111     }
5112   }
5113
5114   /**
5115    * Method invoked by the ChangeListener on the tabbed pane, in other words
5116    * when a different tabbed pane is selected by the user or programmatically.
5117    */
5118   @Override
5119   public void tabSelectionChanged(int index)
5120   {
5121     if (index > -1)
5122     {
5123       alignPanel = alignPanels.get(index);
5124       viewport = alignPanel.av;
5125       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5126       setMenusFromViewport(viewport);
5127     }
5128
5129     /*
5130      * If there is a frame linked to this one in a SplitPane, switch it to the
5131      * same view tab index. No infinite recursion of calls should happen, since
5132      * tabSelectionChanged() should not get invoked on setting the selected
5133      * index to an unchanged value. Guard against setting an invalid index
5134      * before the new view peer tab has been created.
5135      */
5136     final AlignViewportI peer = viewport.getCodingComplement();
5137     if (peer != null)
5138     {
5139       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5140       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5141       {
5142         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5143       }
5144     }
5145   }
5146
5147   /**
5148    * On right mouse click on view tab, prompt for and set new view name.
5149    */
5150   @Override
5151   public void tabbedPane_mousePressed(MouseEvent e)
5152   {
5153     if (e.isPopupTrigger())
5154     {
5155       String msg = MessageManager.getString("label.enter_view_name");
5156       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5157               JOptionPane.QUESTION_MESSAGE);
5158
5159       if (reply != null)
5160       {
5161         viewport.viewName = reply;
5162         // TODO warn if reply is in getExistingViewNames()?
5163         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5164       }
5165     }
5166   }
5167
5168   public AlignViewport getCurrentView()
5169   {
5170     return viewport;
5171   }
5172
5173   /**
5174    * Open the dialog for regex description parsing.
5175    */
5176   @Override
5177   protected void extractScores_actionPerformed(ActionEvent e)
5178   {
5179     ParseProperties pp = new jalview.analysis.ParseProperties(
5180             viewport.getAlignment());
5181     // TODO: verify regex and introduce GUI dialog for version 2.5
5182     // if (pp.getScoresFromDescription("col", "score column ",
5183     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5184     // true)>0)
5185     if (pp.getScoresFromDescription("description column",
5186             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5187     {
5188       buildSortByAnnotationScoresMenu();
5189     }
5190   }
5191
5192   /*
5193    * (non-Javadoc)
5194    *
5195    * @see
5196    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5197    * )
5198    */
5199   @Override
5200   protected void showDbRefs_actionPerformed(ActionEvent e)
5201   {
5202     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5203   }
5204
5205   /*
5206    * (non-Javadoc)
5207    *
5208    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5209    * ActionEvent)
5210    */
5211   @Override
5212   protected void showNpFeats_actionPerformed(ActionEvent e)
5213   {
5214     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5215   }
5216
5217   /**
5218    * find the viewport amongst the tabs in this alignment frame and close that
5219    * tab
5220    *
5221    * @param av
5222    */
5223   public boolean closeView(AlignViewportI av)
5224   {
5225     if (viewport == av)
5226     {
5227       this.closeMenuItem_actionPerformed(false);
5228       return true;
5229     }
5230     Component[] comp = tabbedPane.getComponents();
5231     for (int i = 0; comp != null && i < comp.length; i++)
5232     {
5233       if (comp[i] instanceof AlignmentPanel)
5234       {
5235         if (((AlignmentPanel) comp[i]).av == av)
5236         {
5237           // close the view.
5238           closeView((AlignmentPanel) comp[i]);
5239           return true;
5240         }
5241       }
5242     }
5243     return false;
5244   }
5245
5246   protected void build_fetchdbmenu(JMenu webService)
5247   {
5248     // Temporary hack - DBRef Fetcher always top level ws entry.
5249     // TODO We probably want to store a sequence database checklist in
5250     // preferences and have checkboxes.. rather than individual sources selected
5251     // here
5252     final JMenu rfetch = new JMenu(
5253             MessageManager.getString("action.fetch_db_references"));
5254     rfetch.setToolTipText(MessageManager
5255             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5256     webService.add(rfetch);
5257
5258     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5259             MessageManager.getString("option.trim_retrieved_seqs"));
5260     trimrs.setToolTipText(MessageManager
5261             .getString("label.trim_retrieved_sequences"));
5262     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5263     trimrs.addActionListener(new ActionListener()
5264     {
5265       @Override
5266       public void actionPerformed(ActionEvent e)
5267       {
5268         trimrs.setSelected(trimrs.isSelected());
5269         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5270                 Boolean.valueOf(trimrs.isSelected()).toString());
5271       };
5272     });
5273     rfetch.add(trimrs);
5274     JMenuItem fetchr = new JMenuItem(
5275             MessageManager.getString("label.standard_databases"));
5276     fetchr.setToolTipText(MessageManager
5277             .getString("label.fetch_embl_uniprot"));
5278     fetchr.addActionListener(new ActionListener()
5279     {
5280
5281       @Override
5282       public void actionPerformed(ActionEvent e)
5283       {
5284         new Thread(new Runnable()
5285         {
5286           @Override
5287           public void run()
5288           {
5289             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5290                     .getAlignment().isNucleotide();
5291             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5292                     .getSequenceSelection(), alignPanel.alignFrame, null,
5293                     alignPanel.alignFrame.featureSettings, isNucleotide);
5294             dbRefFetcher.addListener(new FetchFinishedListenerI()
5295             {
5296               @Override
5297               public void finished()
5298               {
5299                 AlignFrame.this.setMenusForViewport();
5300               }
5301             });
5302             dbRefFetcher.fetchDBRefs(false);
5303           }
5304         }).start();
5305
5306       }
5307
5308     });
5309     rfetch.add(fetchr);
5310     final AlignFrame me = this;
5311     new Thread(new Runnable()
5312     {
5313       @Override
5314       public void run()
5315       {
5316         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5317                 .getSequenceFetcherSingleton(me);
5318         javax.swing.SwingUtilities.invokeLater(new Runnable()
5319         {
5320           @Override
5321           public void run()
5322           {
5323             String[] dbclasses = sf.getOrderedSupportedSources();
5324             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5325             // jalview.util.QuickSort.sort(otherdb, otherdb);
5326             List<DbSourceProxy> otherdb;
5327             JMenu dfetch = new JMenu();
5328             JMenu ifetch = new JMenu();
5329             JMenuItem fetchr = null;
5330             int comp = 0, icomp = 0, mcomp = 15;
5331             String mname = null;
5332             int dbi = 0;
5333             for (String dbclass : dbclasses)
5334             {
5335               otherdb = sf.getSourceProxy(dbclass);
5336               // add a single entry for this class, or submenu allowing 'fetch
5337               // all' or pick one
5338               if (otherdb == null || otherdb.size() < 1)
5339               {
5340                 continue;
5341               }
5342               // List<DbSourceProxy> dbs=otherdb;
5343               // otherdb=new ArrayList<DbSourceProxy>();
5344               // for (DbSourceProxy db:dbs)
5345               // {
5346               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5347               // }
5348               if (mname == null)
5349               {
5350                 mname = "From " + dbclass;
5351               }
5352               if (otherdb.size() == 1)
5353               {
5354                 final DbSourceProxy[] dassource = otherdb
5355                         .toArray(new DbSourceProxy[0]);
5356                 DbSourceProxy src = otherdb.get(0);
5357                 fetchr = new JMenuItem(src.getDbSource());
5358                 fetchr.addActionListener(new ActionListener()
5359                 {
5360
5361                   @Override
5362                   public void actionPerformed(ActionEvent e)
5363                   {
5364                     new Thread(new Runnable()
5365                     {
5366
5367                       @Override
5368                       public void run()
5369                       {
5370                         boolean isNucleotide = alignPanel.alignFrame
5371                                 .getViewport().getAlignment()
5372                                 .isNucleotide();
5373                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5374                                 alignPanel.av.getSequenceSelection(),
5375                                 alignPanel.alignFrame, dassource,
5376                                 alignPanel.alignFrame.featureSettings,
5377                                 isNucleotide);
5378                         dbRefFetcher
5379                                 .addListener(new FetchFinishedListenerI()
5380                                 {
5381                                   @Override
5382                                   public void finished()
5383                                   {
5384                                     AlignFrame.this.setMenusForViewport();
5385                                   }
5386                                 });
5387                         dbRefFetcher.fetchDBRefs(false);
5388                       }
5389                     }).start();
5390                   }
5391
5392                 });
5393                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5394                         MessageManager.formatMessage(
5395                                 "label.fetch_retrieve_from",
5396                                 new Object[] { src.getDbName() })));
5397                 dfetch.add(fetchr);
5398                 comp++;
5399               }
5400               else
5401               {
5402                 final DbSourceProxy[] dassource = otherdb
5403                         .toArray(new DbSourceProxy[0]);
5404                 // fetch all entry
5405                 DbSourceProxy src = otherdb.get(0);
5406                 fetchr = new JMenuItem(MessageManager.formatMessage(
5407                         "label.fetch_all_param",
5408                         new Object[] { src.getDbSource() }));
5409                 fetchr.addActionListener(new ActionListener()
5410                 {
5411                   @Override
5412                   public void actionPerformed(ActionEvent e)
5413                   {
5414                     new Thread(new Runnable()
5415                     {
5416
5417                       @Override
5418                       public void run()
5419                       {
5420                         boolean isNucleotide = alignPanel.alignFrame
5421                                 .getViewport().getAlignment()
5422                                 .isNucleotide();
5423                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5424                                 alignPanel.av.getSequenceSelection(),
5425                                 alignPanel.alignFrame, dassource,
5426                                 alignPanel.alignFrame.featureSettings,
5427                                 isNucleotide);
5428                         dbRefFetcher
5429                                 .addListener(new FetchFinishedListenerI()
5430                                 {
5431                                   @Override
5432                                   public void finished()
5433                                   {
5434                                     AlignFrame.this.setMenusForViewport();
5435                                   }
5436                                 });
5437                         dbRefFetcher.fetchDBRefs(false);
5438                       }
5439                     }).start();
5440                   }
5441                 });
5442
5443                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5444                         MessageManager.formatMessage(
5445                                 "label.fetch_retrieve_from_all_sources",
5446                                 new Object[] {
5447                                     Integer.valueOf(otherdb.size())
5448                                             .toString(), src.getDbSource(),
5449                                     src.getDbName() })));
5450                 dfetch.add(fetchr);
5451                 comp++;
5452                 // and then build the rest of the individual menus
5453                 ifetch = new JMenu(MessageManager.formatMessage(
5454                         "label.source_from_db_source",
5455                         new Object[] { src.getDbSource() }));
5456                 icomp = 0;
5457                 String imname = null;
5458                 int i = 0;
5459                 for (DbSourceProxy sproxy : otherdb)
5460                 {
5461                   String dbname = sproxy.getDbName();
5462                   String sname = dbname.length() > 5 ? dbname.substring(0,
5463                           5) + "..." : dbname;
5464                   String msname = dbname.length() > 10 ? dbname.substring(
5465                           0, 10) + "..." : dbname;
5466                   if (imname == null)
5467                   {
5468                     imname = MessageManager.formatMessage(
5469                             "label.from_msname", new Object[] { sname });
5470                   }
5471                   fetchr = new JMenuItem(msname);
5472                   final DbSourceProxy[] dassrc = { sproxy };
5473                   fetchr.addActionListener(new ActionListener()
5474                   {
5475
5476                     @Override
5477                     public void actionPerformed(ActionEvent e)
5478                     {
5479                       new Thread(new Runnable()
5480                       {
5481
5482                         @Override
5483                         public void run()
5484                         {
5485                           boolean isNucleotide = alignPanel.alignFrame
5486                                   .getViewport().getAlignment()
5487                                   .isNucleotide();
5488                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5489                                   alignPanel.av.getSequenceSelection(),
5490                                   alignPanel.alignFrame, dassrc,
5491                                   alignPanel.alignFrame.featureSettings,
5492                                   isNucleotide);
5493                           dbRefFetcher
5494                                   .addListener(new FetchFinishedListenerI()
5495                                   {
5496                                     @Override
5497                                     public void finished()
5498                                     {
5499                                       AlignFrame.this.setMenusForViewport();
5500                                     }
5501                                   });
5502                           dbRefFetcher.fetchDBRefs(false);
5503                         }
5504                       }).start();
5505                     }
5506
5507                   });
5508                   fetchr.setToolTipText("<html>"
5509                           + MessageManager.formatMessage(
5510                                   "label.fetch_retrieve_from", new Object[]
5511                                   { dbname }));
5512                   ifetch.add(fetchr);
5513                   ++i;
5514                   if (++icomp >= mcomp || i == (otherdb.size()))
5515                   {
5516                     ifetch.setText(MessageManager.formatMessage(
5517                             "label.source_to_target", imname, sname));
5518                     dfetch.add(ifetch);
5519                     ifetch = new JMenu();
5520                     imname = null;
5521                     icomp = 0;
5522                     comp++;
5523                   }
5524                 }
5525               }
5526               ++dbi;
5527               if (comp >= mcomp || dbi >= (dbclasses.length))
5528               {
5529                 dfetch.setText(MessageManager.formatMessage(
5530                         "label.source_to_target", mname, dbclass));
5531                 rfetch.add(dfetch);
5532                 dfetch = new JMenu();
5533                 mname = null;
5534                 comp = 0;
5535               }
5536             }
5537           }
5538         });
5539       }
5540     }).start();
5541
5542   }
5543
5544   /**
5545    * Left justify the whole alignment.
5546    */
5547   @Override
5548   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5549   {
5550     AlignmentI al = viewport.getAlignment();
5551     al.justify(false);
5552     viewport.firePropertyChange("alignment", null, al);
5553   }
5554
5555   /**
5556    * Right justify the whole alignment.
5557    */
5558   @Override
5559   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5560   {
5561     AlignmentI al = viewport.getAlignment();
5562     al.justify(true);
5563     viewport.firePropertyChange("alignment", null, al);
5564   }
5565
5566   @Override
5567   public void setShowSeqFeatures(boolean b)
5568   {
5569     showSeqFeatures.setSelected(b);
5570     viewport.setShowSequenceFeatures(b);
5571   }
5572
5573   /*
5574    * (non-Javadoc)
5575    *
5576    * @see
5577    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5578    * awt.event.ActionEvent)
5579    */
5580   @Override
5581   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5582   {
5583     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5584     alignPanel.paintAlignment(true);
5585   }
5586
5587   /*
5588    * (non-Javadoc)
5589    *
5590    * @see
5591    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5592    * .ActionEvent)
5593    */
5594   @Override
5595   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5596   {
5597     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5598     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5599
5600   }
5601
5602   /*
5603    * (non-Javadoc)
5604    *
5605    * @see
5606    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5607    * .event.ActionEvent)
5608    */
5609   @Override
5610   protected void showGroupConservation_actionPerformed(ActionEvent e)
5611   {
5612     viewport.setShowGroupConservation(showGroupConservation.getState());
5613     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5614   }
5615
5616   /*
5617    * (non-Javadoc)
5618    *
5619    * @see
5620    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5621    * .event.ActionEvent)
5622    */
5623   @Override
5624   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5625   {
5626     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5627     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5628   }
5629
5630   /*
5631    * (non-Javadoc)
5632    *
5633    * @see
5634    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5635    * .event.ActionEvent)
5636    */
5637   @Override
5638   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5639   {
5640     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5641     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5642   }
5643
5644   @Override
5645   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5646   {
5647     showSequenceLogo.setState(true);
5648     viewport.setShowSequenceLogo(true);
5649     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5650     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5651   }
5652
5653   @Override
5654   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5655   {
5656     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5657   }
5658
5659   /*
5660    * (non-Javadoc)
5661    *
5662    * @see
5663    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5664    * .event.ActionEvent)
5665    */
5666   @Override
5667   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5668   {
5669     if (avc.makeGroupsFromSelection())
5670     {
5671       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5672       alignPanel.updateAnnotation();
5673       alignPanel.paintAlignment(true);
5674     }
5675   }
5676
5677   public void clearAlignmentSeqRep()
5678   {
5679     // TODO refactor alignmentseqrep to controller
5680     if (viewport.getAlignment().hasSeqrep())
5681     {
5682       viewport.getAlignment().setSeqrep(null);
5683       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5684       alignPanel.updateAnnotation();
5685       alignPanel.paintAlignment(true);
5686     }
5687   }
5688
5689   @Override
5690   protected void createGroup_actionPerformed(ActionEvent e)
5691   {
5692     if (avc.createGroup())
5693     {
5694       alignPanel.alignmentChanged();
5695     }
5696   }
5697
5698   @Override
5699   protected void unGroup_actionPerformed(ActionEvent e)
5700   {
5701     if (avc.unGroup())
5702     {
5703       alignPanel.alignmentChanged();
5704     }
5705   }
5706
5707   /**
5708    * make the given alignmentPanel the currently selected tab
5709    *
5710    * @param alignmentPanel
5711    */
5712   public void setDisplayedView(AlignmentPanel alignmentPanel)
5713   {
5714     if (!viewport.getSequenceSetId().equals(
5715             alignmentPanel.av.getSequenceSetId()))
5716     {
5717       throw new Error(
5718               MessageManager
5719                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5720     }
5721     if (tabbedPane != null
5722             && tabbedPane.getTabCount() > 0
5723             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5724                     .getSelectedIndex())
5725     {
5726       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5727     }
5728   }
5729
5730   /**
5731    * Action on selection of menu options to Show or Hide annotations.
5732    *
5733    * @param visible
5734    * @param forSequences
5735    *          update sequence-related annotations
5736    * @param forAlignment
5737    *          update non-sequence-related annotations
5738    */
5739   @Override
5740   protected void setAnnotationsVisibility(boolean visible,
5741           boolean forSequences, boolean forAlignment)
5742   {
5743     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5744             .getAlignmentAnnotation();
5745     if (anns == null)
5746     {
5747       return;
5748     }
5749     for (AlignmentAnnotation aa : anns)
5750     {
5751       /*
5752        * don't display non-positional annotations on an alignment
5753        */
5754       if (aa.annotations == null)
5755       {
5756         continue;
5757       }
5758       boolean apply = (aa.sequenceRef == null && forAlignment)
5759               || (aa.sequenceRef != null && forSequences);
5760       if (apply)
5761       {
5762         aa.visible = visible;
5763       }
5764     }
5765     alignPanel.validateAnnotationDimensions(true);
5766     alignPanel.alignmentChanged();
5767   }
5768
5769   /**
5770    * Store selected annotation sort order for the view and repaint.
5771    */
5772   @Override
5773   protected void sortAnnotations_actionPerformed()
5774   {
5775     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5776     this.alignPanel.av
5777             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5778     alignPanel.paintAlignment(true);
5779   }
5780
5781   /**
5782    *
5783    * @return alignment panels in this alignment frame
5784    */
5785   public List<? extends AlignmentViewPanel> getAlignPanels()
5786   {
5787     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5788   }
5789
5790   /**
5791    * Open a new alignment window, with the cDNA associated with this (protein)
5792    * alignment, aligned as is the protein.
5793    */
5794   protected void viewAsCdna_actionPerformed()
5795   {
5796     // TODO no longer a menu action - refactor as required
5797     final AlignmentI alignment = getViewport().getAlignment();
5798     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5799     if (mappings == null)
5800     {
5801       return;
5802     }
5803     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5804     for (SequenceI aaSeq : alignment.getSequences())
5805     {
5806       for (AlignedCodonFrame acf : mappings)
5807       {
5808         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5809         if (dnaSeq != null)
5810         {
5811           /*
5812            * There is a cDNA mapping for this protein sequence - add to new
5813            * alignment. It will share the same dataset sequence as other mapped
5814            * cDNA (no new mappings need to be created).
5815            */
5816           final Sequence newSeq = new Sequence(dnaSeq);
5817           newSeq.setDatasetSequence(dnaSeq);
5818           cdnaSeqs.add(newSeq);
5819         }
5820       }
5821     }
5822     if (cdnaSeqs.size() == 0)
5823     {
5824       // show a warning dialog no mapped cDNA
5825       return;
5826     }
5827     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5828             .size()]));
5829     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5830             AlignFrame.DEFAULT_HEIGHT);
5831     cdna.alignAs(alignment);
5832     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5833             + this.title;
5834     Desktop.addInternalFrame(alignFrame, newtitle,
5835             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5836   }
5837
5838   /**
5839    * Set visibility of dna/protein complement view (available when shown in a
5840    * split frame).
5841    *
5842    * @param show
5843    */
5844   @Override
5845   protected void showComplement_actionPerformed(boolean show)
5846   {
5847     SplitContainerI sf = getSplitViewContainer();
5848     if (sf != null)
5849     {
5850       sf.setComplementVisible(this, show);
5851     }
5852   }
5853
5854   /**
5855    * Generate the reverse (optionally complemented) of the selected sequences,
5856    * and add them to the alignment
5857    */
5858   @Override
5859   protected void showReverse_actionPerformed(boolean complement)
5860   {
5861     AlignmentI al = null;
5862     try
5863     {
5864       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5865       al = dna.reverseCdna(complement);
5866       viewport.addAlignment(al, "");
5867       addHistoryItem(new EditCommand(
5868               MessageManager.getString("label.add_sequences"),
5869               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5870               viewport.getAlignment()));
5871     } catch (Exception ex)
5872     {
5873       System.err.println(ex.getMessage());
5874       return;
5875     }
5876   }
5877
5878   /**
5879    * Try to run a script in the Groovy console, having first ensured that this
5880    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5881    * be targeted at this alignment.
5882    */
5883   @Override
5884   protected void runGroovy_actionPerformed()
5885   {
5886     Jalview.setCurrentAlignFrame(this);
5887     groovy.ui.Console console = Desktop.getGroovyConsole();
5888     if (console != null)
5889     {
5890       try
5891       {
5892         console.runScript();
5893       } catch (Exception ex)
5894       {
5895         System.err.println((ex.toString()));
5896         JOptionPane
5897                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5898                         .getString("label.couldnt_run_groovy_script"),
5899                         MessageManager
5900                                 .getString("label.groovy_support_failed"),
5901                         JOptionPane.ERROR_MESSAGE);
5902       }
5903     }
5904     else
5905     {
5906       System.err.println("Can't run Groovy script as console not found");
5907     }
5908   }
5909
5910   /**
5911    * Hides columns containing (or not containing) a specified feature, provided
5912    * that would not leave all columns hidden
5913    *
5914    * @param featureType
5915    * @param columnsContaining
5916    * @return
5917    */
5918   public boolean hideFeatureColumns(String featureType,
5919           boolean columnsContaining)
5920   {
5921     boolean notForHiding = avc.markColumnsContainingFeatures(
5922             columnsContaining, false, false, featureType);
5923     if (notForHiding)
5924     {
5925       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5926               false, featureType))
5927       {
5928         getViewport().hideSelectedColumns();
5929         return true;
5930       }
5931     }
5932     return false;
5933   }
5934 }
5935
5936 class PrintThread extends Thread
5937 {
5938   AlignmentPanel ap;
5939
5940   public PrintThread(AlignmentPanel ap)
5941   {
5942     this.ap = ap;
5943   }
5944
5945   static PageFormat pf;
5946
5947   @Override
5948   public void run()
5949   {
5950     PrinterJob printJob = PrinterJob.getPrinterJob();
5951
5952     if (pf != null)
5953     {
5954       printJob.setPrintable(ap, pf);
5955     }
5956     else
5957     {
5958       printJob.setPrintable(ap);
5959     }
5960
5961     if (printJob.printDialog())
5962     {
5963       try
5964       {
5965         printJob.print();
5966       } catch (Exception PrintException)
5967       {
5968         PrintException.printStackTrace();
5969       }
5970     }
5971   }
5972 }